Sequence Set BrowserShow helpHide help
ABFK00000000.2 Alistipes putredinis DSM 17216
# of Contigs: 20 # of Proteins: 2,742 # of Scaffolds/Chrs: 12 Total length: 2,549,878 bp BioProject: PRJNA19655 BioSample: SAMN00000002 Keywords: WGS Annotation: Contigs Organism: Alistipes putredinis DSM 17216 – show lineagehide lineage Biosource:/mol_type = genomic/strain = DSM 17216 WGS: ABFK02000001:ABFK02000020 Scaffolds: DS499570:DS49958112 scaffolds, total length is 2,550,678 bases Reference:Draft genome sequence of Alistipes putredinis (DSM 17216) : Unpublished – show 7 authorshide authorsSudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M., Liep,D., Gordon,J. Submission:Submitted (07-SEP-2007) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 7 authorshide authorsFulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Mardis,E.R., Wilson,R.K. Submission:Submitted (23-OCT-2007) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 12 authorshide authorsFulton,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 Oct 30, 2007 this sequence version replaced gi:157094014.
The Alistipes putredinis DSM 17216 whole genome shotgun (WGS) project has the project accession ABFK00000000. This version of the project (02) has the accession number ABFK02000000, and consists of sequences ABFK02000001-ABFK02000020.
Alistipes putredinis (GenBank Accession Number for 16S rDNAgene: L16497) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. It has been found in 16S rDNA sequence-based enumerations of the colonic microbiota of adult humans (Eckburg et. al.(2005), Ley et. al. (2006)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 17216). We have collected 11.6X coverage in plasmid end reads and454 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 February 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.