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| C. briggsae Genome Project |
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The C. briggsae genome was sequenced by the Wellcome Trust
Sanger Institute and the Genome Sequencing
Center at the Washington University School of Medicine, St.
Louis. Each Centre has sequenced approximately 1,000,000 whole genome
shotgun reads from plasmids and BAC and fosmid ends. These give a
greater than 10x coverage of the genome.
This C. briggsae sequence (version cb25.agp8) was assembled from 2.05
million whole genome shotgun reads, of which 88.2% are in read pairs.
Using Jim Mullikin's Phusion assembler, reads were first assembled into
contigs on the basis of overlap information, and then into supercontigs
using read pair information to cross gaps. The supercontigs were then
assembled into mapped ultracontigs on the basis of FPC fingerprint
mapping, adding in some material from the previously finished clones to
bridge gaps. Because of the absence of dense chromosomal maps for C.
briggsae, we can not assign these ultracontigs to chromosomal
locations, and so can not give draft chromosome sequences.
In the cb25.agp8 assembly the N50 contig size is 41 kb (half the
sequence is in contigs of this size or greater) and the N50
supercontig (scaffold) size is 1450 kb, so most genes should be
complete. The size of the assembled and FPC mapped genome is 102Mbp in
142 pieces, with an additional 6Mbp not placed on the FPC map in 436
pieces (many highly repetitive). On the basis of comparison to the 12
Mb of previously finished sequence, we estimate that the whole genome
shotgun assembly achieved 98% coverage of the C. briggsae genome. In the
final sequence 270 kb finished fosmid data from 155 accessions was
incorporated to bridge gaps.
Gene prediction data for briggsae is also displayed on the Wormbase site
http://www.wormbase.org/db/seq/gbrowse.
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| Current Release 25.25 |
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Last Update:
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01-07-2003
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Ensembl gene predictions:
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11884
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Genefinder gene predictions:
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13203
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Ensembl gene exons:
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86120
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Ensembl gene transcripts:
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14713
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Contigs:
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5605
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Clones:
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5496
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Base Pairs:
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105835413
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Golden Path Length:
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104573414
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| Example Data Points |
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This release of C. briggsae data is assembled into scaffolds (ultracontigs) and not to chromosomes, so there are no chromosomes available to browse. Use the BLAST, SSAHA, and Search links in the Entry Points section above to locate data.
A few example data points :
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Gene : CBG09431
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Transcript : ENSCBRT00000006437
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Peptide : ENSCBRP00000006437
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Scaffold : cb25.fpc2220
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| Documentation & Help |
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| About Ensembl |
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For context-sensitive help
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| Questions or suggestions? Try |
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Documentation (includes tutorial on direct data access & instructions for installing Ensembl on your own site)
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| Ensembl Links and Site Map |
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