On Nov 9, 2007 this sequence version replaced gi:157834621.
The [Clostridium] scindens ATCC 35704 whole genome shotgun (WGS) project has the project accession ABFY00000000. This version of the project (02) has the accession number ABFY02000000, and consists of sequences ABFY02000001-ABFY02000068.
Clostridium scindens (GenBank Accession Number for 16S rDNA gene: AF262238) is a member of the division Firmicutes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans, it represents, on average, 0.025% of all 16S rDNA sequences and 0.049% of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 35704).
We have collected 9.1X 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. 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).
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.
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.
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