PeroxiBase: a database for large-scale evolutionary analysis of peroxidases

被引：133

作者：

Fawal, Nizar ^{[1
,2
]}

Li, Qiang ^{[1
,2
]}

Savelli, Bruno ^{[1
,2
]}

Brette, Marie ^{[1
,2
]}

Passaia, Gisele ^{[3
]}

Fabre, Maxime ^{[1
,2
]}

Mathe, Catherine ^{[1
,2
]}

Dunand, Christophe ^{[1
,2
]}

机构：

[1] Univ Toulouse, UPS, UMR 5546, Lab Rech Sci Vegetales, Castanet Tolosan, France

[2] CNRS, UMR 5546, Castanet Tolosan, France

[3] Univ Fed Rio Grande do Sul, Dept Genet, BR-91501970 Porto Alegre, RS, Brazil

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / D1期

关键词：

ANNOTATION; GENE;

D O I：

10.1093/nar/gks1083

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：

The PeroxiBase (http://peroxibase.toulouse.inra.fr/) is a specialized database devoted to peroxidases' families, which are major actors of stress responses. In addition to the increasing number of sequences and the complete modification of the Web interface, new analysis tools and functionalities have been developed since the previous publication in the NAR database issue. Nucleotide sequences and graphical representation of the gene structure can now be included for entries containing genomic cross-references. An expert semi-automatic annotation strategy is being developed to generate new entries from genomic sequences and from EST libraries. Plus, new internal and automatic controls have been included to improve the quality of the entries. To compare gene structure organization among families' members, two new tools are available, CIWOG to detect common introns and GECA to visualize gene structure overlaid with sequence conservation. The multicriteria search tool was greatly improved to allow simple and combined queries. After such requests or a BLAST search, different analysis processes are suggested, such as multiple alignments with ClustalW or MAFFT, a platform for phylogenetic analysis and GECA's display in association with a phylogenetic tree. Finally, we updated our family specific profiles implemented in the PeroxiScan tool and made new profiles to consider new sub-families.

引用

页码：D441 / D444

页数：4

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