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Sequence Set Browser

 

ABCD00000000.1 Yersinia pestis CA88-4125

Master
# of Contigs: 8
# of Proteins: 3,851
Total length: 4,658,875 bp
BioProject: PRJNA18241
BioSample: SAMN02403940
Keywords: WGS
Annotation: Contigs
Organism: Yersinia pestis CA88-4125show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = CA88-4125
WGS: ABCD01000001:ABCD01000008
Reference:
Yersinia pestis CA88-4125 whole genome shotgun sequencing project : Unpublished – show 17 authorshide authors
Plunkett,G. III, Anderson,B.D., Burland,V., Cabot,E.L., Glasner,J.D., Mau,B., Neeno-Eckwall,E., Perna,N.T., Bruce,D., Gilna,P., Green,L.D., Keim,P., Munk,A.C., Probert,W.S., Vogler,A.J., Wagner,D.M., Brettin,T.S.
Submission:
Submitted (07-JUN-2007) Genome Center of Wisconsin, University of Wisconsin, Enteropathogen Resource Integration Center (ERIC-BRC), 425G Henry Mall, Madison, WI 53706-1580, USA – show 17 authorshide authors
Plunkett,G. III, Anderson,B.D., Burland,V., Cabot,E.L., Glasner,J.D., Mau,B., Neeno-Eckwall,E., Perna,N.T., Bruce,D., Gilna,P., Green,L.D., Keim,P., Munk,A.C., Probert,W.S., Vogler,A.J., Wagner,D.M., Brettin,T.S.

The Yersinia pestis CA88-4125 whole genome shotgun (WGS) project has the project accession ABCD00000000. This version of the project (01) has the accession number ABCD01000000, and consists of sequences ABCD01000001-ABCD01000008.

Yersinia pestis CA88-4125 was originally isolated in Monterey County, California. This area is very close to San Francisco, where Yersinia pestis is first thought to have become established in native populations of rodents. Subsequent spread of plague to the rest of the western United States probably originated from this region. As such, comparisons of this strain to other North American Y. pestis strains should provide interesting insights into how Y. pestis mutated as it spread across the western United States. Three libraries were constructed with average insert sizes of 2874 bp, 3961 bp, and 4758 bp from which 37463, 21554, and 24262 reads were sequenced, respectively. This amount of sequence represents 10X coverage of the genome. After two rounds of autofinish sequencing, several scaffolds were connected by PCR end sequences and shatter libraries, and a number of duplications were resolved with transposon bombed subclones. Draft sequencing was performed at the Joint Genome Institute (JGI) production genomics facility in Walnut Creek, CA. Two rounds of genome finishing was performed by the JGI at Los Alamos National Laboratory, Los Alamos, NM. Annotation and database submission were carried out by the Enteropathogen Resource Integration Center, Madison, WI (ERIC http://www.ericbrc.org/portal/eric), a Bioinformatics Resource Center supported by the NIH/NIAID. The NIAID funded Bioinformatics Resource Center PathoSystems Resource Integration Center (PATRIC; http://patricbrc.vbi.vt.edu/) is responsible for annotation updates of this record. Plasmids pCD1 and pMT1 are GenBank Accession Numbers CP000722-CP000723.

Contigs
Proteins
Download
GenBank:ABCD01.1.gbff.gz 3 Mb
FASTA:ABCD01.1.fsa_nt.gz 1.4 Mb
ASN.1:ABCD01.1.bbs.gz 2.3 Mb