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We've updated our browsers for the C. remanei and C. brenneri nematode genomes. Both sets of sequence were obtained from the Genome Sequencing Center at Washington University in St. Louis (WUSTL) School of Medicine. The C. remanei assembly (UCSC version caeRem3) corresponds to WUSTL version 15.0.1 dated May 2007. The C. brenneri assembly (UCSC version caePb2) is based on WUSTL version 6.0.1 dated Feb. 2008.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the WUSTL data use policy for usage restrictions and citation information.

We'd like to thank WUSTL for providing the sequence data for these assemblies. The UCSC worm browsers were produced by Hiram Clawson, Brooke Rhead, Pauline Fujita, and Donna Karolchik. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release.

We have released a Genome Browser for the Mar. 2007 assembly of the lamprey genome, Petromyzon marinus. This assembly, UCSC version petMar1, was produced by the Genome Sequencing Center at the Washington University in St. Louis School of Medicine (WUSTL), St. Louis, MO, USA.

Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or Downloads page. The lamprey sequence is made freely available before scientific publication. Please see the WUSTL data use policy for usage restrictions and citation information.

The UCSC Lamprey Genome Browser was produced by Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The Mar. 2006 release of the lancelet genome (Branchiostoma floridae) is now available in the UCSC Genome Browser. This assembly, UCSC version braFlo1, was produced by the DOE Joint Genome Institute (JGI), Walnut Creek, CA, USA.

Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or Downloads page. The lancelet sequence is made freely available before scientific publication. Please see the JGI data release policy for usage restrictions and citation information.

The UCSC Lancelet Genome Browser was produced by Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The Feb. 2008 CavPor3 release of the guinea pig genome (Cavia porcellus) is now available in the UCSC Genome Browser. This assembly, UCSC version cavPor3, was produced by the Broad Institute.

The guinea pig is one of 24 mammals whose genomes are being sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health. While most of these genomes are slated for low-coverage (2X), a limited subset (including the guinea pig genome) are being sequenced to a higher quality of 6-7X.

The guinea pig genome has been sequenced to 6.76X coverage with 95.55% of bases assembled. A total of 3143 scaffolds cover 2,722,377,657 bases (2.17% in gaps), with 50% of the scaffolds having a (N50) length of at least 27,408,292 bases (not including gaps). For more details about the assembly, see the Broad Institute Mammmalian Genome Project page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

The UCSC Guinea Pig Genome Browser was produced by Tim Dreszer, Kate Rosenbloom, Hiram Clawson, Kayla Smith, Robert Kuhn, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

Global Solutions for Infectious Diseases (GSID) has announced the launch of an HIV Data Browser with clinical and viral sequence data from infected subjects in the VAX004 (North American/European) Phase III clinical trial of the AIDSVAX B/B vaccine. The browser, which is a customized version of the UCSC Genome Browser developed by the UCSC Genome Bioinformatics group and hosted by GSID, provides researchers with searchable demographic and clinical data from volunteers who became HIV infected during the VAX004 trial. Using the browser, viral sequences may be aligned with one another or with reference or consensus sequences.

GSID is making these AIDSVAX data and serological samples available to the HIV research community through an agreement with VaxGen and with funding provided by the Bill and Melinda Gates Foundation. Future releases will include the addition of clinical and viral sequence data from infected subjects in the VAX003 (Thai) Phase III clinical trial of AIDSVAX B/E, and immunogenicity data from infected subjects in both the VAX004 and VAX003 trials. The browser may be expanded to include data from uninfected subjects in both trials as well.

For information on accessing the GSID HIV Data Browser and background on the AIDSVAX clinical trials, visit http://www.gsid.org/index02.html.

We'd like to announce the release of a Genome Browser and Blat server for the marmoset genome (Callithrix jacchus). The June 2007 assembly -- WUSTL version Callithrix jacchus-2.0.2, UCSC version calJac1 -- was produced by Washington University St. Louis (WUSTL) School of Medicine Genome Sequencing Center in St. Louis, MO, USA.

C. jacchus, a member of the New World monkey clade, is the most widely studied marmoset. It is a popular non-human primate model due to its small body size and unique biological features, and has contributed to the study of brain function, immunity, reproductive biology and drug toxicity. C. jacchus marmosets typically give birth to twins that are somatic chimeras, i.e. each sibling is the mixture of sibling genotypes. (Excerpted from the WUSTL C. jacchus project page.)

The C. jacchus genome was sequenced to 6X coverage using DNA from a female marmoset provided by the Southwestern National Primate Research Center in San Antonio, TX, USA. DNA from a full brother of the female was used as the source for the CHORI-259 BAC library. This assembly is composed of 49,724 supercontigs containing a total of approximately 3.02 billion bases. For more statistics and details on the assembly process, refer to the WUSTL Callithrix_jacchus-2.0.2 assembly page.

Bulk downloads of the calJac1 sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. The sequence data can also be obtained directly from WUSTL. See the WUSTL data use policy for conditions of use. Please acknowledge WUSTL School of Medicine Genome Sequencing Center in any publications that result from the use of this sequence assembly.

We'd like to thank WUSTL School of Medicine Genome Sequencing Center for providing this assembly. The initial set of marmoset browser annotation tracks were generated by UCSC. The UCSC marmoset Genome Browser team is Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We'd like to introduce the Archaeal Genome Browser Database, a visualization tool and an integrated repository for archaeal functional genomics data. This resource was developed by the Lowe Lab in the UCSC Biomolecular Engineering Department, with key assistance from the UCSC Genome Browser team. The Archaeal Genome Browser Database home page can be accessed via the Archaeal Genomes menu link on the Genome Browser home page.

Currently there are more than 50 completed archaeal genomes, the least studied domain of life. Although archaea and bacteria are both prokaryotes, often co-existing in the same environments, many aspects of archaeal cell biology such as DNA replication, repair, transcription, and translation are homologous to those found in eukaryotes. Some members of archaea are also notable for inhabiting extreme environments, including boiling terrestrial hot springs, black smoker vents at the bottom of the ocean, the ultra briny water of the Dead Sea, and highly acidic drainage water from ore mines, to name a few.

The Archaeal Genome Browsers offer a variety of basic tracks derived from Genbank RefSeq annotation, along with published genome analyses from the Lowe Lab and external groups. The annotations include operon predictions, regulatory sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments, and protein conservation across major phylogenetic groups.

The goal of the Lowe Lab is to make the Archaeal Genome Browser Database a forum for ongoing community-based genome annotation, and they welcome new experimental and bioinformatic analyses. If you would like to contribute data, or have questions or feedback about the database, contact Todd Lowe.

The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Oct. 2007 draft assembly of the Cow genome Bos taurus. This assembly (UCSC version bosTau4) was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) as Baylor release Btau_4.0.

The Btau_4.0 release was produced using the Atlas genome assembly system at BCM HGSC. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 11869 scaffolds (named chrUn.004.*). The mitochondrial sequence (available in the browser as "chrM") was obtained from Genbank accession GI:60101824.

The Btau_4.0 assembly was tested against available bovine sequence data sets (EST sequences and finished BAC sequences) for extent of coverage (completeness). When assembled contigs were tested, over 95% of the sequences in these data sets were found to be represented, indicating that the shotgun libraries used to sequence the genome were comprehensive. Of the 1.04 million EST sequences 95.0% were contained in the assembled contigs. Assuming the ESTs are uniformly distributed throughout the genome, the estimated genome size is 2.73Gb/95% = 2.87Gb. For detailed information on the sequencing and assembly techniques, see the Baylor Bovine Genome Project web page.

For a list of the chromosomes and scaffolds in this assembly, click the "Sequences" link on the cow browser gateway page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have specific conditions for use. The cow annotation tracks were generated by UCSC and collaborators worldwide.

We'd like to thank Baylor College of Medicine for providing this assembly. The UCSC bosTau4 browser and documentation were produced by Hiram Clawson, Brian Raney, and Ann Zweig. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The UCSC Bioinformatics Group announces your chance to bring our hands-on computer workshop on the UCSC Genome Browser to your institution. The seminar is presented by our training partner, OpenHelix.

The 3-1/2-hour introductory tutorial will cover the topics needed to effectively use our tool set, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The workshop material requires knowledge of genomic/biological concepts, but no programming skills are required. Participants will receive slide hand-outs, exercises, and UCSC Genome Browser and Table Browser Quick Reference Cards.

To bring the seminar to your institution, apply on the OpenHelix website. Participating institutions are required only to:

--Provide a computer classroom with internet access. The preferred number of computers is 24 or above. As an alternative to a computer room, the institution may provide a classroom with wireless access and ask participants to bring their own laptops. The seminar can be done in the morning and repeated in the afternoon to reach more users.

--Conduct outreach and communication to participants as necessary.

The number of seminars is limited -- apply today! Contact information: www.openhelix.com or 1-888-861-5051.

About OpenHelix, LLC: OpenHelix provides the genomics knowledge you need when you need it. OpenHelix offers online self-run tutorials, web seminars, and on-site training for institutions and companies on the most powerful and popular free, web-based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs. The company has its headquarters in Seattle, with offices in San Francisco and Boston. Further information can be found at www.openhelix.com or by calling 1-888-861-5051.

The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Jul. 2007 draft assembly of the Sumatran orangutan genome, Pongo pygmaeus abelii. This assembly (UCSC version ponAbe2, WUSTL version Pongo_albelii-2.0.2) was provided by the Genome Sequencing Center at Washington University School of Medicine in St. Louis (WUSTL), MO, USA.

The orangutan genome was sequenced to 6X coverage using a female orangutan known as "Susie" from the Gladys Park Zoo (Brownsville, TX, USA). The combined sequence reads were assembled using PCAP and filtered for all known non-orangutan sequence contaminants. For more details about the assembly, see the orangutan browser gateway page and the WUSTL Pongo abelii web page.

Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum gap size of 30 kb allowed. For a list of the chromosomes in this assembly, click the "Sequences" link on the orangutan browser gateway page. The mitochondrial sequence is also available as the virtual chromosome "chrM".

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have specific conditions for use. The orangutan browser annotation tracks were generated by UCSC and collaborators worldwide.

We'd like to thank WUSTL for providing this assembly. The UCSC ponAbe2 browser and documentation were produced by Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The Genome Browser team is happy to announce new functionality in the main genome browser track display. A new configuration button, "Reverse," now allows users to view the entire browser image flipped right-to-left. This is especially useful when a user's gene of interest aligns on the opposite strand from the reference assembly. Those genes then appear in the 5' to 3' direction.

When the reverse function has been activated, all of the track labels usually displayed on the left side of the track (including the mini-button providing access to configuration options) are displayed on the right side. This allows users to see at a glance which direction is being displayed. All navigation options operate as expected.

Thanks to Mark Diekhans, Ann Zweig, Robert Kuhn and the rest of the engineering team for implementing this feature.

In addition to the openings listed in the 12 Dec. 2007 announcement (see below), the UCSC Genome Browser project is accepting applications for Research Software Architect, a position in the UC Project Scientist academic series. For the job description, qualifications and application information, please see the Center for Biomolecular Science and Engineering website. To ensure full consideration, applications must be received by 22 Jan. 2008.

The UCSC Genome Browser project is currently accepting applications for two positions on our development team: Software Development Engineer (Programmer/Analyst 3) and Biological Database Testing/User Support Technician (Programmer/Analyst 1). We are looking for talented self-motivated individuals who would like to use their skills in computer science, biology, and bioinformatics on a fast-paced project featuring the work of top genomics scientists worldwide.

For a summary of the position details and qualifications, see the entries for Software Developer and Biological Database Testing/User Support Technician on the Center for Biomolecular Science and Engineering (CBSE) website. For detailed job descriptions and application information, go to the UCSC Staff Employment website, click the "Search Postings" link on the sidebar, and type in job #0701419 (Software Developer) or job #0701391 (Testing/User Support Technician).

The latest zebrafish assembly -- Zv7 (UCSC version danRer5, July 2007) -- is now available in the UCSC Genome Browser. The Zv7 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.

This assembly consists of 1,440,582,308 bp in 5,036 fragments. It includes sequence anchored to chromosomes 1-25 and chrM (mitochondrial), as well as 5010 unplaced scaffolds. The assembly was produced by integrating finished clone sequence from the physical map with whole genome shotgun assembly sequence. The N50 size is 1,153,933, n = 277 (i.e. the length such that 50% of the assembled genome lies in blocks of the N50 size or longer). For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project and the track description page for the Assembly track.

The danRer5 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data.

We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Ann Zweig, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

The Sep. 2006 release of the purple sea urchin genome (Strongylocentrotus purpuratus) is now available in the UCSC Genome Browser. This assembly, UCSC version strPur2, was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) and corresponds to their Spur_2.1 assembly.

The Spur_2.1 release was assembled from BAC sequence reads (approximately 2x coverage) and whole genome shotgun reads (6x coverage), and utilizes BAC tiling path information. The BCM HGSC Atlas-2.0 genome assembly system was used to generate this assembly. The total length of all contigs greater than 1kb is 804 Mbp. When the gaps between contigs in scaffolds are included, the total span of the assembly is 907 Mbp. The estimated size of the genome based on the assembly is 814 Mbp.

Compared to previous sea urchin releases, the Spur_2.1 assembly is more continuous and has fewer false duplications; contaminations identified in the previous Spur_2.0 assembly have been removed. This draft assembly may contain errors; therefore, users should exercise caution. Typical errors may include misassemblies of repeat sequences, collapses of repeat regions, and artificial duplications in polymorphic regions. However, base accuracy in contigs is usually very high with most errors near the ends of contigs.

More assembly details can be found in the Spur_2.1 README file and on the BCM HGSC Sea Urchin Genome Project web page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The initial set of strPur2 annotation tracks was generated by UCSC. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The UCSC ENCODE browser for the human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly at http://genome.ucsc.edu/ENCODE/encode.hg18.html or by clicking the ENCODE link in the sidebar menu on this page, then clicking the Regions (hg18) link in the sidebar menu on the ENCODE portal page.

The hg18 ENCODE browser includes 540 data tables in 59 browser tracks that were migrated from the hg17 browser. The hg17 data coordinates were converted to hg18 coordinates using the UCSC liftOver process.

To improve the accessibility of the data, related ENCODE tracks have been gathered into new configuration groupings ("super-tracks") that can be displayed or hidden using a single visiblity control. We have also reduced the number of track groups and have modified some of the group names for clarity. ENCODE tracks with whole-genome data have been moved into the standard browser track groups.

For more information about the hg18 ENCODE data migration, see the News section on the UCSC ENCODE portal page and the UCSC genomeWiki.

The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 37.1, is now available in the UCSC Genome Browser. This version (UCSC version mm9) is considered to be essentially finished.

The Build 37.1 assembly includes approximately 2.6 Gb of sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). In-depth information about this assembly will become available on the NCBI website. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced.

The mm9 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm9 annotation tracks were generated by UCSC and collaborators worldwide. NOTE: To expedite the availability of the mm9 browser on our website, the initial release does not contain the comparative genomics annotations. These will be added to our website as they become available. Also, note that the UCSC mm9 database contains only the reference strain C57BL/6J.

We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm9 team: Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page.

The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Aug. 2006 Btau_3.1 draft assembly of the cow genome. This assembly (UCSC version bosTau3) was provided by Baylor College of Medicine Human Genome Sequencing Center in Houston, TX.

The Btau_3.1 release was produced by the Atlas genome assembly system at Baylor College of Medicine Human Genome Sequencing Center. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 13045 scaffolds (named chrUn.003.*). More information on the Btau_3.1 assembly can be found on the Baylor Bovine Genome Project web page and the Readme file that accompanies this release.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please refer to the Baylor conditions of use regarding these data. The bosTau3 annotation tracks were generated by UCSC and collaborators worldwide.

We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Heather Trumbower, Angie Hinrichs, Kayla Smith, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We've updated our existing nematode browsers--for C. elegans and C. briggsae--to the latest publicly available assemblies. In addition, we've added three new worms to our collection: C. brenneri (Caenorhabditis n. sp. PB2801), C. remanei, and Pristionchus pacificus. The C. elegans sequence was obtained from WormBase; the Genome Sequencing Center at Washington University in St. Louis (WUSTL) provided sequence data for the other four assemblies.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the data use policy for the WUSTL-generated assemblies.

We'd like to thank WUSTL, WormBase, and the Sanger Institute for providing the sequence data for these assemblies. The UCSC worm browsers were produced by Hiram Clawson, Kayla Smith, Brooke Rhead, Ann Zweig, and Donna Karolchik. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release.

The latest D. melanogaster assembly can now be viewed in the UCSC Genome Browser. This version -- Release 5, dated Apr. 2006 (UCSC version dm3) -- was provided by the Berkeley Drosophila Genome Project (BDGP) and combines both euchromatic and heterochromatic sequence. The Release 5.1 annotations (Mar. 2007) were provided by FlyBase.

The six euchromatic arms in this assembly were sequenced and assembled by BDGP from a combination of BAC and whole genome shotgun data, and have been finished to high quality. All euchromatic sequence have been compared to the restriction digest fingerprints in multiple enzymes for validity. The details of this analysis will be described in a forthcoming publication.

Heterochromatic sequence from the Drosophila Heterochromatin Genome Project (DHGP) are also available in this assembly. Scaffolds that could not be unambiguously mapped to a chromosome arm have been concatenated into chrUn. chrUextra contains small scaffolds produced by the Celera shotgun assembler that could not be consistently joined with larger scaffolds. Because some of the chrUextra data are of low quality, researchers are encouraged to contact either BDGP or DHGP for further details on this resource. For more information on this assembly, see the Release 5 assembly release notes.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. We'd like to thank the BDGP, DHGP, and Flybase for providing data for this release. The dm3 Genome Browser was produced by Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik. The D. melanogaster browser annotations were generated by FlyBase, DHGP, and the UCSC Genome Bioinformatics group. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We are pleased to announce the release of new versions of the Conservation and Most Conserved annotation tracks for the Human March 2006 Genome Browser (hg18, NCBI Build 36). The new Conservation track displays multiple alignments of 27 vertebrate species aligned to the human genome, along with measurements of evolutionary conservation across all species in the alignment and a separate measurement of conservation across the placental mammal subset of species in the alignment.

The new track includes:

• 5 new high-quality assemblies -- horse, platypus, lizard, and two fish (stickleback and medaka)
• 6 new low-coverage mammalian genomes -- bushbaby, tree shrew, guinea pig, hedgehog, common shrew, and cat
• 6 updated assemblies -- chimp, cow, chicken, frog, fugu, and zebrafish
• 10 assemblies included in the previous version of the track -- rhesus, mouse, rat, rabbit, dog, armadillo, elephant, tenrec, opossum, and tetraodon

In addition to the expanded species list, the new Conservation track features the following improvements:

• additional filtering of pairwise alignments for each species to reduce paralogous alignments
• information about the quality of aligning species sequence included in the multiple alignment downloads
• new track configuration buttons to assist in selecting which species to display

Bulk data downloads are available from the Genome Browser FTP server (alignments, conservation) or from the Downloads page.

The previous 17-vertebrate versions of the Conservation and Most Conserved tracks remain available on the hg18 Genome Browser as the "17-Way Cons" and "17-Way Most Cons" tracks.

The findings of the ENCODE project have been released to the public today, the culmination of a four-year effort to catalog the biologically functional elements in 1 percent of the human genome. The publications, which include a group paper in the 14 June 2007 issue of Nature and 28 companion papers in the June 2007 issue of Genome Research, were authored by researchers from academic, governmental, and industry organizations located in 11 countries. The Nature issue includes a pull-out poster featuring a screenshot of the UCSC Genome Browser displaying a broad range of the ENCODE data.

In the press release accompanying the publication rollout, NHGRI Director Francis S. Collins is quoted as saying "This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome. Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases."

The main portal for the ENCODE data is the UCSC ENCODE Genome Browser. The analysis effort has been coordinated from Ensembl. Much of the primary data have been deposited in the NCBI GEO and EBI ArrayExpress databases. To access the UCSC Genome Browser ENCODE portal, click the ENCODE link in the left sidebar menu on the Genome Browser home page.

For more information on the ENCODE project, including the consortium's data release and accessibility policies and a list of NHGRI-funded participants, see the NHGRI ENCODE website. To read more about UCSC's role on the project, see the news release on the UCSC Center for Biomolecular Science and Engineering website.

We have released a Genome Browser and Blat server for the Jan. 2007 v5.0.1 draft assembly of Ornithorhynchus anatinus (UCSC version ornAna1) produced by the Genome Sequencing Center at Washington University, St. Louis, MO (WUSTL).

This assembly, which was sequenced using a combination of whole genome shotgun plasmid, fosmid and BAC end sequences, has a coverage of approximately 6X. It is comprised of about 1.84 Gb of actual sequence (excluding gap estimates), with 437 Mb anchored and ordered on chromosomes.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

We'd like to thank WUSTL for providing this assembly. The platypus Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, Brian Raney, and Donna Karolchik. The platypus browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

A Genome Browser and Blat server are now available for the Feb 2007 v1.0 draft assembly (UCSC version anoCar1) of Anolis carolinensis produced by the Broad Institute. This assembly has been sequenced to 6.8X coverage. The draft sequence contains 7,233 scaffolds comprised of nearly 1.74 Gb.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

We'd like to thank the Broad Institute for providing this assembly. The lizard Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik. The lizard browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The dates for the upcoming OpenHelix Genome Browser seminars in Washington, D.C. and Los Angeles, CA have been changed. The following updated announcement includes the new dates:

The UCSC Bioinformatics Group announces three regional seminars and hands-on computer workshops on the UCSC Genome Browser presented by OpenHelix:

• Philadelphia -- Wednesday, 13 June
• Washington. D.C./Baltimore -- Wednesday, 20 June
• Los Angeles -- Wednesday, 27 June

These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. Participants receive a complete set of slide and exercise handouts and printed Quick Reference Cards.

For further information or to make a reservation, visit the OpenHelix website or call 1-888-861-5051. Register early; seating is limited. Academic and student discounts are available.

The Jan. 2007 EquCab1 release of the horse genome (Equus caballus) is now available in the UCSC Genome Browser. This assembly, UCSC version equCab1, was produced by the Broad Institute.

The horse draft genome has been sequenced to 6.8X coverage. Approximately 84% of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn", separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM". For more details about the assembly, see the Broad Institute Horse Genome Project page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

The UCSC Horse Genome Browser was produced by Fan Hsu, Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs, Kate Rosenbloom, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We're happy to announce the release of a Genome Browser and Blat server for the Medaka Version 1.0 draft assembly (Apr. 2006, UCSC version oryLat1). This assembly was produced in Japan by the National Institute of Genetics (NIG) and the University of Tokyo. It is equivalent to Ensembl's Oct. 2005 MEDAKA1 data set.

The v1.0 assembly has been sequenced to 10.6X coverage. It consists of approximately 700.4 million bp (excluding gaps) on chromosomes 1-24. 7,299 scaffolds comprised of nearly 36,500 contigs of unplaced sequence are displayed on the virtual chromosome "chrUn". These contigs are spaced with a 10 bp gap; scaffold gaps are 100 bp in size. The medaka mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM".

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. See the University of Tokyo medaka website for the data release policy for this assembly.

The Medaka browser annotation tracks were generated by UCSC and collaborators worldwide. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release.

OpenHelix will present a free introductory seminar on the Genome Browser during Experimental Biology 2007, April 29-May 1, in Washington, D.C. The tutorial will cover the topics needed to effectively use the Genome Browser, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter.

The seminar will be held on Monday April 30, 4:30-5:30p.m. in Room 204C in the Washington, D.C. Convention Center. It is open to any interested conference attendee with a basic knowledge of genomic/biological concepts; no programming skills are needed.

The tutorial requires no advanced registration or fee. Attendees will receive a free download of the training materials. For more information, see the OpenHelix website or call 1-888-861-5051.

In addition to the tutorial, OpenHelix will be presenting brief introductory overviews of the UCSC Genome Browser and other bioinformatics resources during show hours at Booth 330/332. Stop by the booth for more information and to receive your free Genome Browser Quick Reference Cards.

The UCSC Genome Browser now includes the latest release of the Fugu genome. The v4.0 whole genome shotgun assembly (Oct. 2004, UCSC fr2) was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium led by the JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).

This version has been sequenced to approximately 8.5X coverage. The assembly contains 7,213 scaffolds covering 393,312,790 bp. The UCSC browser displays the scaffolds on the virtual chromosome chrUn with gaps of 1,000 bp between scaffolds. The scaffolds range in size from 2,223 bp to 7,245,445 bp. Fifty percent of the sequence (196,648,171 bp) is contained within 125 scaffolds of size 858,115 or greater (N50). The Fugu mitochondrial sequence is also available as the virtual chromosome chrM (GenBank accession: NC_004299.1).

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have been freely provided by the JGI for use in the UCSC Genome Browser.

Many thanks to the JGI, IMCB, and the International Fugu Genome Consortium for the assembly data. The UCSC Fugu Genome Browser was produced by Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik. The annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We are pleased to announce the release of a new gene prediction set, UCSC Genes, on the latest human Genome Browser (hg18, NCBI Build 36). This annotation, which includes putative non-coding genes as well as protein-coding genes and 99.9% of RefSeq genes, is the next generation of the Known Genes set that UCSC has been providing for several years and supersedes the existing Known Genes annotation on the hg18 assembly.

The UCSC Genes is a moderately conservative prediction set based on data from RefSeq, GenBank, and UniProt. Each entry requires the support of one GenBank RNA sequence plus at least one additional line of evidence, with the exception of RefSeq RNAs, which require no additional evidence. Some of the non-coding transcripts in the set may actually code for protein, but the evidence for the associated protein is weak at best. Compared to RefSeq, this gene set generally has about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants.

A new companion track to UCSC Genes, Alt Events, shows various types of alternative splicing, alternative promoter, and other events that result in more than a single transcript from the same gene. This track is based on an analysis by the txgAnalyse program of splicing graphs produced by the txGraph program.

The UCSC Genes set is produced using a computational pipeline developed at UCSC by Jim Kent, Chuck Sugnet and Mark Diekhans. The programs used to construct the Alt Events data set were written by Jim Kent. For detailed information about the process used to construct the genes set, see the track description page. In upcoming months, we plan to release UCSC Genes sets on several organisms in addition to human. The UCSC Genes annotations will be updated approximately every three months.

As part of this change, we are now using our own UCSC Genes accession numbers as the primary key into the underlying knownGene table, rather than the GenBank mRNA accessions we used in the previous Known Genes prediction set. Note that this may affect external sites with URLs that link into our genes track using the older-style accessions.

We will continue to provide the older Known Genes track on hg18 under the name "Old Known Genes". You may find the following tables useful in referencing the older gene set and converting between the two sets:

• knownGeneOld2: new name for table underlying the old Known Genes (previously called knownGene)
• kgXrefOld2: new name for table that contains data for converting old Known Genes IDs to other IDs (previously called kgXref)
• kg2ToKg3: data for converting old Known Genes IDs to the newer UCSC Genes IDs

We'd like to acknowledge the many people affiliated with the UCSC Genome Bioinformatics group who worked hard to release this new annotation: developers Jim Kent, Mark Diekhans, and Fan Hsu (with technical support from several other engineers in the group); David Haussler; our splendid QA team -- Archana Thakkapallayil, Ann Zweig, Robert Kuhn, Kayla Smith, and Brooke Rhead; our build engineer -- Andy Pohl; and our sysadmin group. We'd also like to thank Chuck Sugnet for his input, the people and organizations maintaining the RefSeq, UniProt, and GenBank databases, and the scientists worldwide who have contributed to them. If you have any questions about this new release, feel free to contact us at genome@soe.ucsc.edu (general questions) or genome-mirror@soe.ucsc.edu (mirror-specific questions).

We have released a Genome Browser and Blat server for the Feb. 2006 v1.0 draft assembly of Gasterosteus aculeatus produced by the Broad Institute.

This assembly has been sequenced to approximately 6X coverage. An estimated 87% of the sequence has been anchored to chromosomes (chrI - chrXXI). Of the remaining unanchored scaffolds, those that could be localized to a chromosome have been concatenated into the virtual chromosome "chrUn" with 1000bp gaps between scaffolds. The stickleback mitochondrial sequence is also available as the virtual chromosome "chrM".

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

The stickleback browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We are pleased to announce the release of a new session management functionality in the Genome Browser, which allows users to save and share browser sessions.

Users are now able to configure their browsers with specific track combinations, including custom tracks, and save the configuraton options. Multiple sessions may be saved for future reference, for comparison of scenarios or for sharing with colleagues. Saved sessions persist for one year after the last access, unless deleted. Custom tracks persist for at least 48 hours after the last time they are viewed.

The new feature may be accessed via the "Sessions" link in the top blue bar in any assembly. To ensure privacy and security, users must login to the genomewiki site and create a username and password. Individual sessions may be designated by the user as either "shared" or "non-shared" to protect the privacy of confidential data.

To avoid having a new shared session from someone else override existing Genome Browser settings, users are encouraged to open a new web-browser instance or to save existing settings in a session before loading a new shared session.

The Sessions feature was written by Angie Hinrichs of the UCSC Genome Bioinformatics Group and released with the assistance of Kayla Smith and Robert Kuhn.

We are pleased to announce the release of a new software tool in the Genome Browser collection, the Genome Graphs tool. Genome Graphs offers the ability to upload and display genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies and homozygosity mapping. The Genome Graphs tool may be accessed from the menu on the UCSC Genome Bioinformatics home page.

The initial release of Genome Graphs includes the following features:

• upload several sets of genome-wide data and display them simultaneously
• click on an area of interest and go directly to the genome browser at that position
• set a significance threshold for your data and view only regions that meet that threshold
• view the genes that exist in areas where your data meet your significance threshold

For more information about the Genome Graphs tool, visit the Gateway page or consult the Getting Started on Genome Graphs section in the User's Guide.

Genome Graphs was written by Jim Kent of the UCSC Genome Bioinformatics Group and released with the assistance of Ann Zweig.

The Mar. 2006 release of Felis catus (UCSC version felCat3) is now available in the Genome Browser. This assembly was produced by The Broad Institute of MIT/Harvard and Agencourt Bioscience.

The felCat3 genome has been sequenced to 2X coverage and consists of 217,790 scaffolds. The total contig length for this assembly is approximately 1.6 Gb spanning nearly 4.0 Gb (with 60.1% in gaps). There are 749,376 contigs, with an N50 length of 2,506 bases. There are 149,283 supercontigs, with an N50 length of 49,769 bases (not including gaps). The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The felCat3 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. Please review the guidelines for using the cat assembly data.

Many thanks to The Broad Institute for providing these data. The UCSC cat Genome Browser was produced by Heather Trumbower, Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana Thakkapallayil. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by OpenHelix:

• San Francisco, CA -- Wednesday, 31 January
• Seattle, WA -- Thursday, 1 February
• New York City, NY -- Tuesday, 13 February
• Cleveland, OH -- Wednesday, 14 February

These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. Participants receive a complete set of slide and exercise handouts and printed Quick Reference Cards.

For further information or to make a reservation, visit the OpenHelix website or call 1-888-861-5051. Register early; seating is limited. Academic and student discounts are available.

The UCSC Genome Bioinformatics group has launched a wiki site for sharing information about the UCSC Genome Browser and its data. The wiki -- at http://genomewiki.ucsc.edu -- provides an informal forum for our browser users, mirror sites, and staff to discuss topics of interest in the genome biology field and exchange usage tips, scripts/programs, and notes about mirroring the Genome Browser and working with the Genome Browser source.

As with most wiki pages, general users are welcome to edit and add pages (login required). Please note that all content created on the genomewiki site becomes a public resource; content persists in the history of a page even after it has been deleted.

OpenHelix will present a free seminar on the UCSC Genome Browser at the American Heart Association's Scientific Sessions 2006 in Chicago, IL, on 12 Nov. from 7:00 - 8:30 p.m. The seminar will be held in the Hyatt Regency Conference Center, Room CC21, 2233 South Martin Luther King Drive, Chicago, IL.

The introductory tutorial will cover the topics needed to effectively use the Genome Browser including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The jointly-sponsored seminar will also include an introduction to VISTA comparative genomics tools.

The session is open to anyone attending the AHA Scientific Sessions; no registration or fee is required. Participants should have a basic knowledge of genomic/biological concepts, but no programming skills are needed. Attendees will receive a free download of training materials, and refreshments will be served. This event is not part of the official Scientific Sessions 2006 as planned by the AHA Committee on Scientific Sessions Program.

OpenHelix will also be presenting brief introductory overviews of the Genome Browser and other resources during show hours at booth 2464. Stop by the booth for more information and to receive your free Quick Reference Cards for the Genome Browser and Table Browser.

We have enhanced one of the popular tools in the Genome Browser collection: the custom tracks utility. The new custom tracks tool provides a more user-friendly interface and increased flexibility for creating and managing your custom tracks.

The initial release of this upgraded tool includes the following features:

• Add and display multiple custom tracks simultaneously via URL, file or text
• Add to, delete and modify the uploaded custom tracks set using a new track management interface
• Load and manage custom tracks from multiple assemblies
• Create and upload description pages for custom tracks
• Custom tracks will now persist on our server for 48 hours after last access (rather than 8 hours)

For more information about the new custom tracks functionality, see the Genome Browser Users's Guide. The hgCustom CGI was written by Kate Rosenbloom with the assistance of Archana Thakkapallayil, Ann Zweig and other members of the UCSC Genome Bioinformatics Group.

The Jan. 2005 rheMac1 draft assembly has been moved from the main Genome Browser website to our archive server. The data remain available for browsing and downloading, although blat services are no longer supported.

The UCSC Genome Browser now includes the latest draft assembly of the opossum genome. The Jan. 2006 release of Monodelphis domestica (UCSC version monDom4) was sequenced and assembled by The Broad Institute, Cambridge, MA, USA.

This draft, which has approximately 6.5X coverage, has an assembly length of nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, and Un. The N50 of the genome including gaps is 104,359 bp; the N50 without gaps is 107,990. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The monDom4 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. Please review the guidelines for using the opposum assembly data.

Many thanks to The Broad Institute for providing these data. The UCSC opossum Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

We have updated the Chicken Genome Browser to include the May 2006 v2.1 assembly (UCSC version galGal3) produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, MO, USA (WUSTL). The source of this sequence was a female inbred Red Jungle Fowl (Gallus gallus), the ancestor of domestic chickens. The chicken genome is the first of the avian genomes to be sequenced.

In this assembly, 198,000 additional reads covering all contig ends and regions of low quality have been added to the original assembly's 6.6X coverage. Approximately 95% of the sequence has been anchored to chromosomes, which include autosomes 1-24, 26-28, and 32, and sex chromosomes W and Z. (In contrast to mammals, the female chicken is heterogametic (ZW) and the male is homogametic (ZZ).) The remaining unanchored contigs that could be localized to a chromosome have been concatenated into the virtual chromosomes "chr*_random", separated by gaps of 10,000 bp. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn_random", separated by gaps of 100 bp to reduce the total size of chrUn_random. The chicken mitochondrial sequence is also available as the virtual chromosome "chrM".

Although centromere positions are indicated on this assembly, little is known of their exact sequence. The centromeres of 18 chromosomes were tentatively localized based on FISH hybridization using BAC clones, genetic markers flanking the centromeres in coordination with mapping gaps in the physical map, repetitive sequence content, and analysis of proximity to the constrictions of the mitotic metaphase chromosomes. For more information on the process used to create the chromosomal sequences and assign centromere locations, see the WUSTL Gallus gallus assembly release notes.

Bulk downloads of the chicken sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. These data have specific conditions for use.

We'd like to thank WUSTL, who provided the sequence, physical map, assembly, and assembly/map for this release. The genetic mapping and linkage analysis were produced through a collaborative effort of labs in The Chicken Mapping Consortium. The chicken browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of acknowledgements. The UCSC Chicken Genome Browser was produced by Angie Hinrichs, Kayla Smith, and Donna Karolchik.

We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. The Mar. 2006 assembly -- labeled Chimp Build 2 Version 1 (UCSC version panTro2) -- was produced by the Chimpanzee Sequencing and Analysis Consortium.

This 6X whole genome assembly contains sequence from the initial 4X chimpanzee assembly described and analyzed in Nature (The Chimpanzee Sequencing and Analysis Consortium, 2005), with additional 2X sequence generated, assembled, and assigned to chromosomes by the Genome Sequencing Center of Washington University School of Medicine, St. Louis, MO, USA.

The whole genome shotgun data were derived primarily from the donor Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center in Atlanta, GA, USA. The reads were assembled using the whole-genome assembly program PCAP. For information about the assembly process, see the panTro2 Gateway page.

This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It is composed of 265,882 contigs with an N50 length of 29 kb and 44,460 supercontigs with an N50 length of 9.7 Mb. The total contig length, not including estimated gap sizes, is 2.97 Gb. Of that total, 2.82 Gb of sequence have been ordered and oriented along specific chimpanzee chromosomes, 107 Mb have been placed in chr*_random, and 50 Mb remain in chrUn.

A major difference between this assembly and the previous Nov. 2003 version is the chromosomal numbering scheme, which has been changed to reflect a new standard that preserves orthology with human chromomes. Proposed by E.H. McConkey in 2004, the new numbering convention was subsequently endorsed by the International Chimpanzee Sequencing and Analysis Consortium. This standard assigns the identifiers "2a" and "2b" to the two chimp chromosomes that fused in the human genome to form chromosome 2. Note that the genome assembly shown in the Nov. 2003 panTro1 Genome Browser retains the older numbering scheme, in which these chromosomes are numbered 12 and 13.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The complete set of sequence reads is available at the NCBI trace archive. These data have specific conditions for use.

We'd like to thank the International Chimpanzee Sequencing and Analysis Consortium, Washington University at St. Louis School of Medicine Genome Sequencing Center, and the Broad Institute for providing this sequence. We'd also like to acknowledge the UCSC team who worked on this release: Kate Rosenbloom, Brian Raney, Hiram Clawson, Ann Zweig, Archana Thakkapallayil, and Donna Karolchik. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide.

The UCSC Genome Bioinformatics group has released a Genome Browser for the v3.4 rat (Rattus norvegicus) genome. This assembly--UCSC version rn4, November 2004--was produced by the Atlas group at Baylor Human Genome Sequencing Center (HGSC) as part of the Rat Genome Sequencing Consortium.

The sequence was assembled using a hybrid approach that combines the clone-by-clone and whole genome shotgun methods. The assembly is a minor update to version 3.3 that spliced in 54.6 Mb finished BAC sequences; the overall statistics are unchanged from releases 3.0 to 3.4.

The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Cancer Agency Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC Rat Genome Project web page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data are made available with specific conditions for use.

We'd like to thank the Rat Genome Sequencing Consortium and the Baylor HGSC for providing this assembly. We'd also like to acknowledge the UCSC team who produced the rn4 Genome Browser: Angie Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The rn4 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The v.4.1 Xenopus tropicalis assembly is now available on the UCSC Genome Browser. This whole genome shotgun assembly (xenTro2, August 2005) was generated by the U.S. DOE Joint Genome Institute (JGI) using the Jazz assembler. It contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half the genome is contained in 272 scaffolds, each of at least 1.56 Mb in length.

In this release, some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed by the JGI and placed in a separate directory. The X. tropicalis assembly will be improved over the coming year by additional sequencing of large insert clones, targeted gap closure, and the incorporation of physical and genetic mapping information as it becomes available.

For more information about the 4.1 assembly, see the JGI X. tropicalis website.

The xenTro2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use.

Many thanks to the JGI and the other institutions who contributed to the sequencing and mapping effort for this release. The xenTro2 Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik. The xenTro2 annotation tracks were generated by UCSC and collaborators worldwide. See the credits page for a detailed list of the organizations and individuals who contributed to this release.

The latest zebrafish assembly -- Zv6 (UCSC version danRer4, March 2006) -- is now available in the UCSC Genome Browser. The Zv6 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.

This assembly consists of 1,626,077,335 bp in 6.653 scaffolds (N50 = 1,247,221 bp) with a sequence coverage of approximately 6.5-7x. The sequence has been anchored to chromosomes 1-25, chrM (mitochondrial), chrNA_random, and chrUn_random. For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project.

The danRer4 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data.

We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 36, is now available in the UCSC Genome Browser. This version (UCSC version mm8) is considered to be essentially finished.

The Build 36 assembly includes approximately 2.6 Gb of sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). For in-depth information about the process used to assemble this version, see the NCBI website. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced. Note that the UCSC mm8 database contains only the reference strain C57BL/6J.

The mm8 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm8 annotation tracks were generated by UCSC and collaborators worldwide.

We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm8 team: Hiram Clawson, Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke Rhead, Archana Thakkapallayil, and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page.

The latest human genome reference sequence assembly (NCBI Build 36.1, March 2006) is now available as database hg18 in the UCSC Genome Browser. This sequence, which was obtained from NCBI, was produced by the International Human Genome Sequencing Consortium.

The hg18 assembly contains four alternate haplotype regions:

• chr22_h2_hap1 -- an alternate chromosome 22 assembly that contains the CYP2D6 gene (NT_113959.1). CYP2D6 is deleted in the reference assembly.
• chr5_h2_hap1 -- a chromosome 5 alternate assembly of the SMN1 gene region (NT_113801.1, NT_113802.1).
• chr6_cox_hap1 -- an A1-B8-DR3 alternate haplotype assembly of the chromosome 6 MHC region based on sequence data from the COX library (NT_113891.1).
• chr6_qbl_hap2 -- an A26-B18-DR3 alternate haplotype assembly of the chromosome 6 MHC region based on sequence data from the QBL library (NT_113892.1, NT_113893.1, NT_113894.1, NT_113895.1, NT_113896.1, NT_113897.1).

See the Wellcome Trust Sanger Institute MHC Haplotype Project web site for additional information on the chr6 alternate haplotype assemblies.

The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) at chrY:1-2709520 and chrY:57443438-57772954. These sequences were taken from the corresponding regions in the X chromosome and are exact duplications of the X chromosome sequences.

For further information on NCBI Build 36.1, see the NCBI Build 36.1 release notes.

Bulk downloads of the data are available from the UCSC downloads server via ftp or http. We recommend that you use ftp or rsync for downloading large or multiple files.

We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the entire UCSC Genome Browser staff for contributing to this release. Fan Hsu led the UCSC engineering effort; QA was headed up by Ann Zweig.

The April 2005 release of the Purple Sea Urchin genome (Strongylocentrotus purpuratus) is now available in the UCSC Genome Browser. This assembly, UCSC version strPur1, was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) and corresponds to their Spur_0.5 whole genome shotgun assembly.

This release was assembled from whole genome shotgun reads using the Atlas genome assembly system at the BCM HGSC. Several whole genome shotgun libraries, with inserts of 2-6 kb, were used to produce the data. About 7 million reads were assembled, representing about 800 Mb of sequence and about 6x coverage of the (clonable) sea urchin genome. Highly repeated sequences were assembled separately into reptigs and merged into the genome assembly. Sequences from BAC clones were omitted from this assembly and will be placed in a subsequent version of the draft sequence.

This is a draft sequence and may contain errors; therefore, users should exercise caution. Typical errors in draft genome sequences include misassemblies of repeated sequences, collapses of repeated regions, and unmerged overlaps (e.g. due to polymorphisms) creating artificial duplications. However, base accuracy in contigs (contiguous blocks of sequence) is usually very high with most errors near the ends of contigs.

More assembly details can be found in the Spur_0.5 README file and on the BCM HGSC Sea Urchin Genome Project web page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The strPur1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by OpenHelix:

• Houston, TX -- Tuesday, 14 March
• Austin, TX -- Wednesday, 15 March
• Washington, DC -- Tuesday, 18 April
• Miami, FL -- Wednesday, 19 April

These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. Participants receive a complete set of slide and exercise handouts and printed Quick Reference Cards.

For further information or to make a reservation, visit the OpenHelix website or call 1-888-861-5051. Register early; seating is limited. Academic and student discounts are available.

The latest zebrafish assembly -- Zv5 (UCSC version danRer3, May 2005) -- is now available in the UCSC Genome Browser and Blat server. The Zv5 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.

This assembly consists of 1,630,306,866 bp in 16,214 scaffolds (N50 = 1,116,981 bp) with a sequence coverage of approximately 6.5-7x. The assembly has been tied to the fingerprint contig map (data freeze 15th February, 2005) and contains 699 Mb from 4,519 sequenced clones.

The danRer3 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data.

We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

The latest rhesus macaque (Macaca mulatta) draft assembly—v.1.0, Mmul_051212—is now available in the UCSC Genome Browser. This version (UCSC rheMac2) was sequenced and assembled by the Macaque Genome Sequencing Consortium led by the Baylor College of Medicine Human Genome Sequencing Center, in collaboration with the Genome Sequencing Center at Washington University School of Medicine in St. Louis and the J. Craig Venter Institute Joint Technology Center.

The rhesus macaque follows the human and chimpanzee as the third primate and first Old World monkey to have its genome sequenced. Overall, the rhesus genome shares approximately 92 to 95 precent of its sequence with the human, compared with the chimp at 98 precent. Because of its genetic, physiologic, and metabolic similarities to the human and chimp, the rhesus is an ideal reference point for comparisons among the three primates.

The groups in the Macaque Genome Sequencing Consortium produced preliminary assemblies of the genome data using different and complementary approaches. The resulting data were combined into a single, high-density "melded" assembly by a team at J. Craig Venter Institute. This collaboration made use of published rhesus maps, the BAC fingerprint map from the Michael Smith Genome Sciences Centre, and the human reference genome sequence. The v.1.0 assembly covers about 93 percent of the rhesus genome. For more information about the rheMac2 assembly, see the Baylor Rhesus Monkey Project web page.

The rheMac2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

Many thanks to Baylor College of Medicine, the Macaque Genome Sequencing Consortium, and the other institutions who contributed to the sequencing and mapping effort of the v.1.0 release. The UCSC Rhesus Genome Browser was produced by Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The initial set of rheMac2 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

The October 2005 D. sechellia assembly (UCSC version droSec1) is now available in the UCSC Genome Browser. This version was sequenced and assembled by the Broad Institute of MIT and Harvard.

Downloads of the droSec1 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The initial set of droSec1 annotation tracks were generated by UCSC.

Many thanks to the Broad Institute for providing the sequence and assembly of this genome. The UCSC D. sechellia Genome Browser was produced by Angie Hinrichs, Kayla Smith and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 11 January 2006 - D. yakuba Browser Update

The latest D. yakuba assembly is now available in the UCSC Genome Browser. This version — Release 2.0, dated Nov. 2005 (UCSC version droYak2) — was sequenced and assembled by the Genome Sequencing Center, Washington University (WUSTL) School of Medicine in St. Louis.

The whole genome shotgun (WGS) assembly includes both raw shotgun data and data from two rounds of automated, directed read selection, which has improved the sequence quality and narrowed or (in some instances) closed gaps. For more assembly information and statistics, see the WUSTL Genome Sequencing Center Drosophila yakuba web page.

Downloads of the droYak2 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The initial set of droYak2 annotation tracks was generated by UCSC.

Thanks to the Genome Sequencing Center at WUSTL School of Medicine for providing the sequence and assembly of this genome. The droYak2 Genome Browser was produced by Angie Hinrichs, Jennifer Jackson and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the D. persimilis genome. The Oct. 2005 release (UCSC version droPer1) was sequenced and assembled by the Broad Institute of MIT and Harvard. The D. persimilis assembly joins nine other Drosophila species featured in the UCSC Genome Browser.

Downloads of the droPer1 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The droPer1 annotation tracks were generated by UCSC and collaborators worldwide.

Thanks to the Broad Institute for providing the sequence and assembly of this genome. The UCSC D. persimilis Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

UCSC has updated the dog Genome Browser to include the May 2005 v2.0 assembly (UCSC version canFam2) sequenced and assembled by the Broad Institute of MIT and Harvard and Agencourt Bioscience. The whole genome shotgun sequence is based on 7.6X coverage of the dog genome which includes more than 98% of the euchromatic genome.

The dog genome, which contains approximately 2.5 billion base pairs, is similar in size to the genomes of humans and other mammals. The boxer breed was selected for the initial sequencing effort, based on the lower variation rate in its genome relative to other breeds. In addition to the boxer, samples from several other dog breeds were used to generate a set of single nucleotide polymorphisms (SNPs) to facilitate disease studies. The SNPs are available from the Broad Institute dog SNP web page. For more information about the dog draft assembly, see the Broad Institute Dog Genome Sequencing Project web page.

The dog sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use.

Many thanks to the Broad Institute of MIT and Harvard, Agencourt Bioscience, and the other institutions who contributed to the sequencing, assembly, and mapping efforts. The canFam2 Genome Browser team included Angie Hinrichs, Jennifer Jackson, and Donna Karolchik. See the credits page for a detailed list of the organizations and individuals who contributed to this release.

The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 35 (UCSC version mm7), is now available in the UCSC Genome Browser.

The Build 35 assembly includes approximately 2.6 Gb of sequence, of which about 2.2 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI Build 35 Data web page. Please note that the UCSC mm7 database contains only the reference strain C57BL/6J.

The mm7 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm7 annotation tracks were generated by UCSC and collaborators worldwide.

We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm7 team: Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page.

We are pleased to announce the release of a new software tool in the Genome Browser collection, the VisiGene Image Browser. VisiGene offers the ability to view in situ images, allowing examination of expression patterns at both the tissue and cellular levels. The browser serves as a virtual microscope that lets viewers retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. The VisiGene Browser may be accessed from the menu on the UCSC Genome Bioinformatics home page or through a link on the details pages of Known Genes for which a VisiGene annotation exists.

The initial release of VisiGene includes the following image collections:

• Mouse in situ images from the Jackson Lab Gene Expression Database (GED)
• Transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology
• Mouse head and brain in situ images from NCBI's Gene Expression Nervous System Atlas (GENSAT) database
• Xenopus laevis in situ images from the National Institute for Basic Biology (NIBB) XDB project

We hope to integrate images from the Allen Brain Atlas into the VisiGene collection within a few months.

For more information about VisiGene, visit the VisiGene Gateway page or consult the Using the VisiGene Image Browser section in the User's Guide.

We'd like to thank the organizations listed above for permitting us to add their images to the VisiGene database. VisiGene was written by Jim Kent and Galt Barber of the UCSC Genome Bioinformatics Group. Contact Jim if you have an image set you'd like to contribute for display.

We have released a new annotation track — Allen Brain Atlas Probes — that may be found in the Expression and Regulation section of the latest mouse and human assemblies (mm6 and hg17). The Allen Brain Atlas (ABA) is an extensive database of high resolution in situ hybridization images of adult male mouse brains covering the majority of genes. This track provides a link to the ABA images for each probe. For more information about the ABA, see the description page that accompanies this track.

We'd like to thank the Allen Institute for Brain Science, and Susan Sunkin in particular, for coordinating with UCSC on this annotation.

OpenHelix will be presenting a one-hour seminar, "Introduction to the UCSC Genome Browser", at the American Society of Human Genetics (ASHG) 2005 meeting on 26 October, 6:30-7:30 p.m. The introductory tutorial will cover the topics needed to effectively use the Genome Browser, including basic search functionality and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The class, which is open to all registered ASHG attendees, does not require programming skills, although a basic knowledge of genomic and biological concepts is recommended.

The free tutorial will be conducted at the Grand America Hotel, Audubon Room. Snacks and beverages will be served. Attendees will receive a free download of training materials. For further information, visit www.openhelix.com or call 1-888-861-5051.

The UCSC Genome Bioinformatics Group has added the Drosophila grimshawi genome to the collection of fly genomes available in the UCSC Genome Browser. This assembly (UCSC version droGri1, Aug. 2005) was produced by Agencourt Bioscience Corporation in Beverly, MA, USA, using the Arachne assembler.

The droGri1 assembly contains 25,052 scaffolds ranging in size from 196 bases to 14,170,260 bases.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser Credits page.

We'd like to thank Agencourt Bioscience Corporation for providing this assembly. The UCSC droGri1 browser was produced by Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the