Brugia malayi: Difference between revisions
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* 2K : bulk of the sequence @TIGR | * 2K : bulk of the sequence @TIGR | ||
* 15-20 K @TIGR | * 15-20 K @TIGR | ||
* 8,000 BAC clones @Children's Hospital Oakland Research Institute. | * 8,000 BAC clones @Children's Hospital Oakland Research Institute. (!!! no NCBI TA submission) | ||
* [http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?&cmd=retrieve&val=SPECIES_CODE%20%3D%20%22BRUGIA%20MALAYI%22&retrieve=Submit NCBI TA] | * [http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?&cmd=retrieve&val=SPECIES_CODE%20%3D%20%22BRUGIA%20MALAYI%22&retrieve=Submit NCBI TA] | ||
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/brugia_malayi/ NCBI TA FTP] | * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/brugia_malayi/ NCBI TA FTP] | ||
Revision as of 20:03, 18 August 2008
Articles
Genome Info
- 6 chromosomes: 1-5, XY
- ~ 90M, 30% GC, 32% coding, 15% repeats
Other sequences
- mitochondrion finished: 13,657 bp; 24% GC
- Wolbachia endosymbiont strain TRS from Brugia malayi strain wMel complete: 1,080,084 bp; 34%GC (New England Biolabs)
- Wolbachia endosymbiont strain wMel progress (TIGR)
Genome Project
- NCBI Genome project
- NCBI AAQA00000000 AAQA01000001-AAQA01029808
* 26,879 good ctgs * 2,927 contaminants (Example: AAQA01001321 : mouse 99%id hits)
- TIGR Genome project (TRS strain)
Traces
Libraries: * 2K : bulk of the sequence @TIGR * 15-20 K @TIGR * 8,000 BAC clones @Children's Hospital Oakland Research Institute. (!!! no NCBI TA submission)
Trace summary:
* all: 1,260,215
* TRACE_TYPE_CODE
* WGS: 1,258,277
* TRANSPOSON: 1,437
* PRIMER_WALK 501
* CENTER NAME
* TIGR: 856,624
* JCVI 403,591
* NO BACS !!!; max INSERT_SIZE=23K
Assemblies
TIGR
- 9X coverage, 856K Sanger traces => 8,200 scaff & 29,808 ctg (avg. scaff=~10K & avg ctg=~3K)
- "scaffolds totaling ~71 Mb of data with a further ~17.5 Mb of contigs not integrated into any scaffold (orphan contigs)" (Science 2007)