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FP-TDI SNP genotyping


Data Downloads for C. briggsae

Thanks to Wormbase, the Genome Sequencing Center, Jim Mullikin, and other collaborators, we have developed a number of resources to augment C. briggsae's utility as a model organism for genetics. Be sure to right-click and select 'Save Target As' to download these files.

Chromosome Assembly (cb3)
Reference The new Hillier/Waterston "cb3" sequence assembly from Wormbase, which is by chromosome, as a single FASTA file (gzipped).
Repeat-Masked The "cb3" sequence assembly from Wormbase, with repeats masked to lower case using our custom library (gzipped FASTA).
SNP-marked The repeat-masked "cb3" assembly with ssaha-SNP predictions marked by IUPAC ambiguity code (gzipped FASTA).
BLAST DB A WU-BLAST database (3 files) built from the repeat-masked "cb3" assembly (gzipped tarchive).
Ultracontig Assembly (cb25.agp8)
Repeat-Masked The cb25.agp8 (AF16) sequence from Wormbase, modified only so that repetitive regions are in lower case (gzipped fasta).
SNP-marked The cb25.agp8 (AF16) sequence from Wormbase, repeat-masked and with ambiguity codes marking HK104 build 3 SNP positions (gzipped fasta).
HK104 strain HK104-specific, repeat-masked sequence constructed by replacing the canonical base with the strain allele at HK104 build 3 SNP loci (gzipped fasta).
Fingerprint Map The Genome Sequencing Center's AGP file (updated Sep-2005) in which supercontigs are mapped to FPC's (text). The old version is still available.
Gene Predictions These are "best" C. briggsae gene predictions that have been selected from the raw gene set on several criteria (Stein et al. 2003).
SNP Discovery
HK104 SNPs (build 4) The results of SSAHA-SNP discovery in 13,632 random sequence reads from the HK104 mapping strain using the canonical (AF16) sequence. HK104 SNPs from the previous releases build 3 and build 2 are still available.
VT847 SNPs (build 4) The results of SSAHA-SNP discovery in 14,976 random sequence reads from VT847 using the canonical (AF16) sequence. This is the first release of VT847 SNPs.
HK105 SNPs (build 4) The results of SSAHA-SNP discovery in 2,112 random sequence reads from HK105 using the canonical (AF16) sequence. This is the first release of HK105 SNPs.
PB800 SNPs (build 4) The results of SSAHA-SNP discovery in 384 random sequence reads from PB800 using the canonical (AF16) sequence. This is the first release of PB800 SNPs.
Assays and Primers
RFLP Assays (v2.0) Updated! Restriction Fragment Length Polymorphism assays for snip-SNPs identified in the HK104 strain (SNP build 4). This replaces the previous set generated by Todd Harris.
PLP Assays (v3.0) PCR Fragment Length Polymorphism assays for small (7 - 49 bp) AF16-HK104 indels detected by ssahaSNP. Previous versions ( 2.0 and 1.0 are still available.
VT847 PLP Assays PCR Fragment Length Polymorphism assays for small (7 - 30 bp) AF16-VT847 indels detected by ssahaSNP. Please note, genetic map values are estimates based on HK104 data.
Indel Assays (v1.0) New! PCR assays for moderate-size (50-2,000 bp) AF16-HK104 indels detected by our BreakPointRead algorithm.
Repeat Library A custom RepeatMasker library for C. briggsae-specific repetitive sequences, containing briggsae/elegans and simple repeats in both orientations (.lib file). The old version with briggsae-specific repeats only on one strand only is available here.
Genotyping Primers Updated! FP-TDI genotyping assays designed at standard protocols for HK104 SNPs (b4). Also available in zipped and gzipped formats. The previous release is still available.
Genetic Map
Genetic Map v3.3 The latest version of the C. briggsae genetic map, covering ~85% of the genome (text). SNP coordinates were obtained by BLASTing primer sequences to the cb25.agp8 assembly from Wormbase. The previous version (v3.1) of the map is still available.
Mapped SNPs Updated! Chromosome coordinates, contig positions, and primer sequences for the SNPs in the genetic map.
Raw Data (Jul 2005) Genotype data from Cross 1 used to construct the initial genetic map (text).
Raw Data (Nov 2005) Genotype data from Dr. Gupta's F2 mutants used to enhance the genetic map (text).
Genetic Map v2.5 The previous (Sep 05) version of the C. briggsae genetic map (text).
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