Photo courtesy of NHGRI (press photos)
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Callithrix jacchus Photo courtesy of NHGRI (press photos) |
The Jun. 2007 Callithrix jacchus draft assembly (WUSTL version Callithrix jacchus-2.0.2) was produced by the Washington University St. Louis (WUSTL) School of Medicine Genome Sequencing Center in St. Louis, MO, USA and the Baylor College of Medicine (BCM) Human Genome Sequencing Center in Houston, TX, USA.
A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the Marmoset genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| Contig12371 | Displays all of contig 12371 | |
| Contig3759:130,210-140,209 | Displays ten thousand bases of contig 3759 | |
| Contig2815:171328+1500 | Displays a region of Contig 2815 that spans 1500 bases, starting with position 171328 | |
| | ||
| EF215092 | Displays region of mRNA with GenBank accession number EF215092 | |
| EH380513 | Displays region of EST with GenBank accession EH380513 | |
| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| datson | Lists mRNAs deposited by scientist named Datson | |
| Fuchs,E. | Lists mRNAs deposited by co-author E. Fuchs | |
| Use this last format for author queries. Although GenBank requires the search format Fuchs E, internally it uses the format Fuchs,E.. | ||
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. The combined sequence reads were assembled using PCAP and filtered for all known non-marmoset sequence contaminants and unscaffolded singleton contigs of less than 2 kb in length. This assembly differs from the previous 2.0.1 assembly (which is not featured in the UCSC Genome Browser) in that 586 reads containing untrimmed vector sequence were removed from contig ends, resulting in 34 contigs less than 2 kb in length.
The 2.0.2 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.
WUSTL includes the following release notes with this assembly: "This preliminary assembly is being made available to the community while the assembly continues to be refined. This is a draft assembly with limited quality assessment and thus the data is provided "as is". Once the assembly has been quality screened, scaffolded and localized by chromosome, they will be submitted to GenBank and the various genome browsers."
Bulk downloads of the calJac1 sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. See the data use policy for conditions of use. Please acknowledge the WUSTL School of Medicine Genome Sequencing Center and the BCM Human Genome Sequencing Center in any publications that result from the use of this sequence assembly.
We'd like to thank WUSTL and BCM for providing this assembly. The initial set of marmoset browser annotation tracks were generated by UCSC. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.