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Sequence Set Browser

 

ACBY00000000.2 Subdoligranulum variabile DSM 15176

Master
# of Contigs: 91
# of Proteins: 3,381
# of Scaffolds/Chrs: 11
Total length: 3,237,471 bp
BioProject: PRJNA18181
BioSample: SAMN00008862
Keywords: WGS
Annotation: Contigs
Organism: Subdoligranulum variabile DSM 15176show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = DSM 15176
WGS: ACBY02000001:ACBY02000091
Scaffolds: GG704769:GG704779
11 scaffolds, total length is 3,245,471 bases
Submission:
Submitted (14-JAN-2009) 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.
Submission:
Submitted (30-SEP-2009) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 27 authorshide authors
Weinstock,G., Sodergren,E., Clifton,S., Fulton,L., Fulton,B., Courtney,L., Fronick,C., Harrison,M., Strong,C., Farmer,C., Delahaunty,K., Markovic,C., Hall,O., Minx,P., Tomlinson,C., Mitreva,M., Nelson,J., Hou,S., Wollam,A., Pepin,K.H., Johnson,M., Bhonagiri,V., Nash,W.E., Warren,W., Chinwalla,A., Mardis,E.R., Wilson,R.K.
Submission:
Submitted (14-DEC-2009) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 27 authorshide authors
Weinstock,G., Sodergren,E., Clifton,S., Fulton,L., Fulton,B., Courtney,L., Fronick,C., Harrison,M., Strong,C., Farmer,C., Delahaunty,K., Markovic,C., Hall,O., Minx,P., Tomlinson,C., Mitreva,M., Nelson,J., Hou,S., Wollam,A., Pepin,K.H., Johnson,M., Bhonagiri,V., Nash,W.E., Warren,W., Chinwalla,A., Mardis,E.R., Wilson,R.K.

On Oct 5, 2009 this sequence version replaced gi:223960798.

The Subdoligranulum variabile DSM 15176 whole genome shotgun (WGS) project has the project accession ACBY00000000. This version of the project (02) has the accession number ACBY02000000, and consists of sequences ACBY02000001-ACBY02000091.

Subdoligranulum variabile (GenBank Accession Number for 16S rDNA gene: AJ518869) 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, 0.532% of all 16S rDNA sequences and 1.048% of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 15176). 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. 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 work was supported by the National Human Genome Research Institute and the NIH Roadmap Human Microbiome Project [http://nihroadmap.nih.gov/hmp/]. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Genome Coverage: 23.9x Sequencing Technology: 454 Annotation was added to the contigs in December 2009. Product names were updated in August 2012.

Contigs
Proteins
Download
GenBank:ACBY02.1.gbff.gz 2.3 Mb
FASTA:ACBY02.1.fsa_nt.gz 971.9 kb
ASN.1:ACBY02.1.bbs.gz 1.8 Mb