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Sequence Set Browser

 

AAVL00000000.2 Eubacterium ventriosum ATCC 27560

Master
# of Contigs: 38
# of Proteins: 2,802
# of Scaffolds/Chrs: 27
Total length: 2,869,695 bp
BioProject: PRJNA18159
BioSample: SAMN00627091
Keywords: WGS
Annotation: Contigs
Organism: Eubacterium ventriosum ATCC 27560show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = ATCC 27560
WGS: AAVL02000001:AAVL02000038
Scaffolds: DS264262:DS264288
27 scaffolds, total length is 2,870,795 bases
Reference:
Draft genome sequence of Eubacterium ventriosum (ATCC 27560) : Unpublished – show 7 authorshide authors
Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M., Liep,D., Gordon,J.
Submission:
Submitted (05-DEC-2006) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 7 authorshide authors
Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Mardis,E.R., Wilson,R.K.
Submission:
Submitted (27-MAR-2007) 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.

On Apr 11, 2007 this sequence version replaced gi:118776260.

The Eubacterium ventriosum ATCC 27560 whole genome shotgun (WGS) project has the project accession AAVL00000000. This version of the project (02) has the accession number AAVL02000000, and consists of sequences AAVL02000001-AAVL02000038.

Eubacterium ventriosum (GenBank accession number for 16S rRNA gene: L34421) is a member of the division Firmicutes. It represents 0.04% of the total number of microbial 16S rDNA sequences found in the gut (Eckburg et. al. Science 308, 1635 (2005)) and 0.08% of the sequences sequenced within its division. The sequenced strain was obtained from ATCC (ATCC 27560). Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xl sequencers was devised and implemented to generate the draft genome sequences. 15-20X sequence coverage of 454 reads and 4X sequence coverage of 3730 reads were collected. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted to 800 bp linked reads ('superreads') with 400 bp overlap with neighboring linked reads, in silico. Finally, PCAP (Huang, et al, Genome Research, 13:2164, (2003)) was used to assemble the super-reads and the conventional 3730 reads. 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. RNA genes were determined using tRNAscan-SE 1.23 or Rfam v0.1. 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 June 2007. 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:AAVL02.1.gbff.gz 2.1 Mb
FASTA:AAVL02.1.fsa_nt.gz 853.4 kb
ASN.1:AAVL02.1.bbs.gz 1.6 Mb