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Sequence Set Browser

 

ABXJ00000000.1 Collinsella stercoris DSM 13279

Master
# of Contigs: 177
# of Proteins: 2,529
# of Scaffolds/Chrs: 35
Total length: 2,399,821 bp
BioProject: PRJNA19665
BioSample: SAMN00008814
Keywords: WGS
Annotation: Contigs
Organism: Collinsella stercoris DSM 13279show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = DSM 13279
WGS: ABXJ01000001:ABXJ01000177
Scaffolds: DS995473:DS995507
35 scaffolds, total length is 2,475,429 bases
Reference:
Draft genome sequence of Collinsella stercoris (DSM 13279) : Unpublished – show 7 authorshide authors
Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M., Liep,D., Gordon,J.
Submission:
Submitted (01-OCT-2008) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 12 authorshide authors
Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Pepin,K.H., Johnson,M., Thiruvilangam,P., Bhonagiri,V., Nash,W.E., Mardis,E.R., Wilson,R.K.

The Collinsella stercoris DSM 13279 whole genome shotgun (WGS) project has the project accession ABXJ00000000. This version of the project (01) has the accession number ABXJ01000000, and consists of sequences ABXJ01000001-ABXJ01000177.

Collinsella stercoris (GenBank Accession Number for 16S rDNA gene: AB031061) is a member of the Actinobacteria division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 13279). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of one half plate of a Roche 454 FLX paired end library run with a Q20 coverage of 32.9X. This sequenced strain is part of a comprehensive, sequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine, the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled 'Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)' (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMISeq.pdf). These studies are supported by National Human Genome Research Institute. Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. For answers to your questions regarding this assembly or project, or any other GSC genome project, please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. Annotation was added to the contigs in October 2008. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Product names were updated in August 2012.

Contigs
Proteins
Download
GenBank:ABXJ01.1.gbff.gz 1.9 Mb
FASTA:ABXJ01.1.fsa_nt.gz 721.7 kb
ASN.1:ABXJ01.1.bbs.gz 1.4 Mb