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PeroxiBase: a database for large-scale evolutionary analysis of peroxidases
Nizar Fawal1, Qiang Li, Bruno Savelli
1Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, France.
Nucleic Acids Research
|November 28, 2012
Summary
PeroxiBase is an updated peroxidase database featuring new analysis tools for stress response research. Enhanced functionalities improve data quality and comparative gene structure analysis for peroxidase families.
Area of Science:
- Biochemistry and Molecular Biology
- Bioinformatics and Computational Biology
Background:
- Peroxidases are crucial proteins involved in cellular stress responses.
- Databases are essential for organizing and analyzing biological sequence data.
Purpose of the Study:
- To update and enhance the PeroxiBase database with new features and analysis tools.
- To improve the quality and accessibility of peroxidase family data.
Main Methods:
- Database redevelopment with a new web interface and improved data quality controls.
- Development of new analysis tools including CIWOG for intron comparison and GECA for gene structure visualization.
- Implementation of an expert semi-automatic annotation strategy for generating new entries.
- Enhancement of the multicriteria search tool and integration with analysis platforms like ClustalW, MAFFT, and phylogenetic analysis tools.
Main Results:
- PeroxiBase now includes nucleotide sequences and graphical gene structures.
- New tools facilitate comparison of gene structure organization and sequence conservation.
- The database supports advanced queries, multiple sequence alignments, and phylogenetic analysis.
- Updated and new family-specific profiles are available for the PeroxiScan tool.
Conclusions:
- The enhanced PeroxiBase provides a more comprehensive and user-friendly resource for peroxidase research.
- New functionalities facilitate in-depth analysis of peroxidase gene structures and evolutionary relationships.
- The database supports the ongoing study of stress responses and related biological processes.
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