Photo courtesy of Eric Haag, All Rights Reserved.
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Caenorhabditis briggsae Photo courtesy of Eric Haag, All Rights Reserved. |
The Caenorhabditis briggsae genome assembly is based on sequence version cb25.agp8 deposited into WormBase as of August 2005.
A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST, or a gene identifier, chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the C. briggsae genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
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| chrI | Displays all of chromosome I | |
| chrI:1-1000000 | Displays the first million bases of chrI | |
| R02870 | Displays region of EST associated with GenBank accession R02870 | |
| U48289 | Displays the region associated with the mRNA accession U48289 | |
| protein phosphatase PP2C | Lists only records pertaining to protein phophatase PP2C | |
| Kimble,J. | Lists mRNAs deposited by co-author J. Kimble | |
| Use this last format for author queries. Although GenBank requires the search format Kimble J, internally it uses the format Kimble,J.. | ||
This version was assembled from 2.05 million whole genome shotgun (WGS) reads, of which 88.2% were in read pairs. The sequence reads were generated at Washington University School of Medicine's Genome Sequencing Center and the Sanger Centre (Hinxton, UK). The Phusion (Mullikin, J) assembler was used to assemble the WGS reads into contigs based on overlap information, and then into supercontigs using read pair information to cross gaps. These supercontigs were assembled into mapped ultracontigs based on FPC fingerprint mapping (generated at Washington University School of Medicine's Genome Sequencing Center), with material from previously finished clones used to bridge gaps. Using the sequence data to choose primers along major ultracontigs, a genetic map (Ray Miller, Washington University School of Medicine) was constructed which yielded 6 chromosomes. The genetic mapping data along with data from 1:1 elegans:briggsae orthologs were used to refine ultracontigs and to order and orient the sequences along the C. briggsae chromosomes.
The six chromosomes are named: chrI, chrII, chrIII, chrIV, chrV and chrX, containing 89,604,507 bp of ordered and oriented sequence. An additional 11,714,720 bp of sequence is localized to a specific chromosome but not ordered and displayed on the artifical chr*_random chromosomes. 7,825,149 bp of sequence is unordered and not localized, displayed on the chrUn artifical chromosome.
The sequencing centers estimate that this whole genome shotgun assembly achieved 98% coverage of the genome.
The cb2 sequence and annotation data may be downloaded from the UCSC Genome Browser FTP server or Downloads web page. The sequence data have specific conditions for use. The cb2 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.