Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

被引：482

作者：

Winsor, Geoffrey L. ^{[1
]}

Lam, David K. W. ^{[1
]}

Fleming, Leanne ^{[1
]}

Lo, Raymond ^{[1
]}

Whiteside, Matthew D. ^{[1
]}

Yu, Nancy Y. ^{[1
]}

Hancock, Robert E. W. ^{[2
]}

Brinkman, Fiona S. L. ^{[1
]}

机构：

[1] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada

[2] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z4, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

AERUGINOSA PAO1; MUTANT LIBRARY; OPEN SOFTWARE; SEQUENCE; PREDICTION; ARCHIVE;

D O I：

10.1093/nar/gkq869

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：

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented for other genera-level research communities.

引用

页码：D596 / D600

页数：5

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