PHAST: A Fast Phage Search Tool

被引：1580

作者：

Zhou, You ^{[1
]}

Liang, Yongjie ^{[2
]}

Lynch, Karlene H. ^{[1
]}

Dennis, Jonathan J. ^{[1
]}

Wishart, David S. ^{[1
,2
,3
]}

机构：

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

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

[3] Natl Inst Nanotechnol NINT, Natl Res Council, Edmonton, AB T6G 2E8, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

加拿大健康研究院;

关键词：

TRANSFER-RNA GENES; IDENTIFICATION; PREDICTION; PROPHAGES; DATABASE; PROGRAM; FINDER;

D O I：

10.1093/nar/gkr485

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：

PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage 'cornerstone' feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage 'quality' and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com.

引用

页码：W347 / W352

页数：6

共 19 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] Killing cancer cells by targeted drug-carrying phage nanomedicines [J].

Bar, Hagit ;

Yacoby, Iftach ;

Benhar, Itai .

BMC BIOTECHNOLOGY, 2008, 8 (1)

[3]

Bose M., 2006, In Silico Biology, V6, P223

[4] Prophages and bacterial genomics: what have we learned so far? [J].

Casjens, S .

MOLECULAR MICROBIOLOGY, 2003, 49 (02) :277-300

[5] Novel approaches to developing new antibiotics for bacterial infections [J].

Coates, A. R. M. ;

Hu, Y. .

BRITISH JOURNAL OF PHARMACOLOGY, 2007, 152 (08) :1147-1154

[6]

Ester M., 1996, DENSITY BASED ALGORI, DOI DOI 10.5555/3001460.3001507

[7]

FOUTS DE, 2004, INFEC DIS S, P71

[8] Phage_Finder:: Automated identification and classification of prophage regions in complete bacterial genome sequences [J].

Fouts, Derrick E. .

NUCLEIC ACIDS RESEARCH, 2006, 34 (20) :5839-5851

[9] ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences [J].

Laslett, D ;

Canback, B .

NUCLEIC ACIDS RESEARCH, 2004, 32 (01) :11-16

[10] Prophinder: a computational tool for prophage prediction in prokaryotic genomes [J].

Lima-Mendez, Gipsi ;

Van Helden, Jacques ;

Toussaint, Ariane ;

Leplae, Raphael .

BIOINFORMATICS, 2008, 24 (06) :863-865

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