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Sequence Set Browser


AMEN00000000.1 Aggregatibacter actinomycetemcomitans Y4

# of Contigs: 121
# of Proteins: 2,343
# of Scaffolds/Chrs: 87
Total length: 2,185,821 bp
BioProject: PRJNA67199
BioSample: SAMN02436929
Keywords: WGS
Annotation: Contigs
Organism: Aggregatibacter actinomycetemcomitans Y4show lineagehide lineage
/culture_collection = ATCC:43718
/host = Homo sapiens
/isolation_source = oral cavity, subgingival dental plaque
/mol_type = genomic
/strain = Y4
WGS: AMEN01000001:AMEN01000121
Scaffolds: KB290837:KB290923
87 scaffolds, total length is 2,186,501 bases
Submitted (10-MAY-2012) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 26 authorshide authors
Weinstock,G., Sodergren,E., Lobos,E.A., Fulton,L., Fulton,R., Courtney,L., Fronick,C., O'Laughlin,M., Godfrey,J., Wilson,R.M., Miner,T., Farmer,C., Delehaunty,K., Cordes,M., Minx,P., Tomlinson,C., Chen,J., Wollam,A., Pepin,K.H., Bhonagiri,V., Zhang,X., Suruliraj,S., Warren,W., Mitreva,M., Mardis,E.R., Wilson,R.K.

The Aggregatibacter actinomycetemcomitans Y4 whole genome shotgun (WGS) project has the project accession AMEN00000000. This version of the project (01) has the accession number AMEN01000000, and consists of sequences AMEN01000001-AMEN01000121.

Aggregatibacter actinomycetemcomitans Y4 is a member of the Proteobactera division of the domain Bacteria and has been isolated from the oral cavity. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Bacterial strain (ATCC 43718) was obtained from American Type Culture Collection (P.O. Box 1549, Manassas, VA 20108 USA). Source DNA provided by Floyd E. Dewhirst and Jacques Izard (The Forsyth Institute, Department of Molecular Genetics, 245 First St, Cambridge, Massachusetts, 02142). Funded by NIDCR DE016937, 'A Foundation for the Oral Microbiome and Metagenome'. Coding sequences were predicted using GeneMark v3.3 and Glimmer3 v3.02. Intergenic regions not spanned by GeneMark and Glimmer3 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 v8.1. The final gene set is processed through several programs such as Kegg (Release 56), psortB (Version 3.0.3) and Interproscan (Version 4.7) to determine possible function. Gene product names are determined by BER (Version 2.5). Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. The National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) is funding the sequence characterization of the Aggregatibacter actinomycetemcomitans Y4 genome.

Finishing Goal : High-Quality Draft
Current Finishing Status : High-Quality Draft
Assembly Method : Velvet v. 1.1.04
Genome Coverage : 477x
Sequencing Technology : Illumina
GenBank:AMEN01.1.gbff.gz 1.7 Mb
FASTA:AMEN01.1.fsa_nt.gz 664.9 kb
ASN.1:AMEN01.1.bbs.gz 1.3 Mb