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).
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| 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.
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| 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.
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| 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.
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| 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.
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| 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). |
