BacMap: an up-to-date electronic atlas of annotated bacterial genomes

被引：16

作者：

Cruz, Joseph ^{[1
]}

Liu, Yifeng ^{[1
]}

Liang, Yongjie ^{[1
]}

Zhou, You ^{[2
]}

Wilson, Michael ^{[1
]}

Dennis, Jonathan J. ^{[2
]}

Stothard, Paul ^{[3
]}

Van Domselaar, Gary ^{[4
]}

Wishart, David S. ^{[1
,2
]}

机构：

[1] Univ Alberta, Dept Comp Sci, Edmonton, AB T6G 2E8, Canada

[2] Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E8, Canada

[3] Univ Alberta, Dept Agr Food & Nutr Sci, Edmonton, AB T6G 2E8, Canada

[4] Publ Hlth Agcy Canada, Natl Microbiol Lab, Winnipeg, MB R3E 3R2, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

加拿大健康研究院;

关键词：

DATABASE; GENERATION; RESOURCE;

D O I：

10.1093/nar/gkr1105

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Originally released in 2005, BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains fully labeled, zoomable and searchable chromosome maps for essentially all sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. The latest release of BacMap (http://bacmap.wishartlab.com/) now contains data for more than 1700 bacterial species (similar to 10x more than the 2005 release), corresponding to more than 2800 chromosome and plasmid maps. All bacterial genome maps are now supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap also contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images (when available). Improved data browsing and searching tools have also been added to allow more facile filtering, sorting and display of the chromosome maps and their contents.

引用

页码：D599 / D604

页数：6

共 22 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2]

[Anonymous], NUCL ACIDS RES

[3]

[Anonymous], NUCL ACIDS RES

[4] GenBank [J].

Benson, Dennis A. ;

Karsch-Mizrachi, Ilene ;

Lipman, David J. ;

Ostell, James ;

Sayers, Eric W. .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D32-D37

[5] DNAPlotter: circular and linear interactive genome visualization [J].

Carver, Tim ;

Thomson, Nick ;

Bleasby, Alan ;

Berriman, Matthew ;

Parkhill, Julian .

BIOINFORMATICS, 2009, 25 (01) :119-120

[6] WHOLE-GENOME RANDOM SEQUENCING AND ASSEMBLY OF HAEMOPHILUS-INFLUENZAE RD [J].

FLEISCHMANN, RD ;

ADAMS, MD ;

WHITE, O ;

CLAYTON, RA ;

KIRKNESS, EF ;

KERLAVAGE, AR ;

BULT, CJ ;

TOMB, JF ;

DOUGHERTY, BA ;

MERRICK, JM ;

MCKENNEY, K ;

SUTTON, G ;

FITZHUGH, W ;

FIELDS, C ;

GOCAYNE, JD ;

SCOTT, J ;

SHIRLEY, R ;

LIU, LI ;

GLODEK, A ;

KELLEY, JM ;

WEIDMAN, JF ;

PHILLIPS, CA ;

SPRIGGS, T ;

HEDBLOM, E ;

COTTON, MD ;

UTTERBACK, TR ;

HANNA, MC ;

NGUYEN, DT ;

SAUDEK, DM ;

BRANDON, RC ;

FINE, LD ;

FRITCHMAN, JL ;

FUHRMANN, JL ;

GEOGHAGEN, NSM ;

GNEHM, CL ;

MCDONALD, LA ;

SMALL, KV ;

FRASER, CM ;

SMITH, HO ;

VENTER, JC .

SCIENCE, 1995, 269 (5223) :496-512

[7] Ensembl 2011 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Chen, Yuan ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gordon, Leo ;

Hendrix, Maurice ;

Hourlier, Thibaut ;

Johnson, Nathan ;

Kaehaeri, Andreas ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Kokocinski, Felix ;

Kulesha, Eugene ;

Larsson, Pontus ;

Longden, Ian ;

McLaren, William ;

Overduin, Bert ;

Pritchard, Bethan ;

Riat, Harpreet Singh ;

Rios, Daniel ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sobral, Daniel ;

Spudich, Giulietta ;

Tang, Y. Amy ;

Trevanion, Stephen ;

Vandrovcova, Jana ;

Vilella, Albert J. ;

White, Simon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Zamora, Jorge ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard ;

Fernandez-Suarez, Xose M. ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Parker, Anne ;

Proctor, Glenn .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D800-D806

[8] The value of complete microbial genome Sequencing (you get what you pay for) [J].

Fraser, CM ;

Eisen, JA ;

Nelson, KE ;

Paulsen, IT ;

Salzberg, SL .

JOURNAL OF BACTERIOLOGY, 2002, 184 (23) :6403-6405

[9] PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species [J].

Gillespie, Joseph J. ;

Wattam, Alice R. ;

Cammer, Stephen A. ;

Gabbard, Joseph L. ;

Shukla, Maulik P. ;

Dalay, Oral ;

Driscoll, Timothy ;

Hix, Deborah ;

Mane, Shrinivasrao P. ;

Mao, Chunhong ;

Nordberg, Eric K. ;

Scott, Mark ;

Schulman, Julie R. ;

Snyder, Eric E. ;

Sullivan, Daniel E. ;

Wang, Chunxia ;

Warren, Andrew ;

Williams, Kelly P. ;

Xue, Tian ;

Yoo, Hyun Seung ;

Zhang, Chengdong ;

Zhang, Yan ;

Will, Rebecca ;

Kenyon, Ronald W. ;

Sobral, Bruno W. .

INFECTION AND IMMUNITY, 2011, 79 (11) :4286-4298

[10] KEGG for representation and analysis of molecular networks involving diseases and drugs [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Furumichi, Miho ;

Tanabe, Mao ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D355-D360

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