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Sequence Set Browser

 

ABXW00000000.1 Providencia alcalifaciens DSM 30120

Master
# of Contigs: 79
# of Proteins: 4,022
Total length: 4,029,346 bp
BioProject: PRJNA29297
BioSample: SAMN00008853
Keywords: WGS
Annotation: Contigs
Organism: Providencia alcalifaciens DSM 30120show lineagehide lineage
Biosource:
/culture_collection = DSM:30120
/mol_type = genomic
/strain = DSM 30120
WGS: ABXW01000001:ABXW01000079
Reference:
Draft genome sequence of Providencia alcalifaciens (DSM 30120) : Unpublished – show 7 authorshide authors
Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M., Liep,D., Gordon,J.
Submission:
Submitted (16-OCT-2008) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 11 authorshide authors
Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Pepin,K.H., Johnson,M., Bhonagiri,V., Nash,W.E., Mardis,E.R., Wilson,R.K.

The Providencia alcalifaciens DSM 30120 whole genome shotgun (WGS) project has the project accession ABXW00000000. This version of the project (01) has the accession number ABXW01000000, and consists of sequences ABXW01000001-ABXW01000079.

Providencia alcalifaciens (GenBank Accession Number: DQ885261), is a member of the division Proteobacteria of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 30120). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of a one quarter plate 454 Titanium fragment library with a Q20 coverage of 28.8X. 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 November 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 June 2013.

Contigs
Proteins
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GenBank:ABXW01.1.gbff.gz 2.9 Mb
FASTA:ABXW01.1.fsa_nt.gz 1.2 Mb
ASN.1:ABXW01.1.bbs.gz 2.2 Mb