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Sequence Set Browser

 

AAXA00000000.2 Dorea formicigenerans ATCC 27755

Master
# of Contigs: 16
# of Proteins: 3,277
Total length: 3,186,031 bp
BioProject: PRJNA18155
BioSample: SAMN00000008
Keywords: WGS
Annotation: Contigs
Organism: Dorea formicigenerans ATCC 27755show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = ATCC 27755
WGS: AAXA02000001:AAXA02000016
Reference:
Draft genome sequence of Dorea formicigenerans(ATCC 27755) : Unpublished – show 7 authorshide authors
Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M., Liep,D., Gordon,J.
Submission:
Submitted (26-SEP-2007) 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 (08-OCT-2007) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 13 authorshide authors
Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Pepin,K.H., Johnson,M., Thiruvilangam,P., Bhonagiri,V., Nash,W.E., Wang,C., Mardis,E.R., Wilson,R.K.

On Oct 10, 2007 this sequence version replaced gi:157834380.

The Dorea formicigenerans ATCC 27755 whole genome shotgun (WGS) project has the project accession AAXA00000000. This version of the project (02) has the accession number AAXA02000000, and consists of sequences AAXA02000001-AAXA02000016.

Dorea formicigenerans (GenBank Accession Number for 16S rRNA gene: L34619) is a member of the Firmicutes division of the domain bacteria. In one comprehensive 16S rDNA sequence- based enumeration of the colonic microbiota of three healthy adult humans, it represents, on average, 0.617% of all 16S rDNA sequences and 1.215% of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 27755). We have collected 7.5X coverage in plasmid end reads and 454 reads. We have performed one round of automated sequence improvement (pre-finishing), along with manual improvement that includes breaking apart any mis-assembly, and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. 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. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally, PCAP (Huang, et al, Genome Research, 13:2164, (2003)) was used to assemble the super-reads and the conventional 3730xl capillary 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. 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. 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. 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 January 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
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GenBank:AAXA02.1.gbff.gz 2.3 Mb
FASTA:AAXA02.1.fsa_nt.gz 957.7 kb
ASN.1:AAXA02.1.bbs.gz 1.8 Mb