PeroxiBase peroxidase family database

PeroxiBase peroxidase family database catalogs and annotates peroxidase nucleotide and protein sequences with gene-structure information to support comparative genomics, functional annotation, and phylogenetic analyses of peroxidase superfamilies.

Key Features:

• Enhanced Sequence Repository: Collection of nucleotide and protein sequences from peroxidase families with genomic cross-references linking gene and protein structures.
• Analysis tools (CIWOG and GECA): CIWOG detects common introns among family members and GECA visualizes gene structure overlaid with sequence conservation for comparative genomics.
• Semi-automatic annotation strategy: Expert-driven, semi-automatic annotation of entries generated from genomic sequences and expressed sequence tag (EST) libraries.
• Quality control measures: Internal and automatic controls applied to maintain and improve the quality of database entries.
• Advanced search and query integration: Multicriteria search and BLAST queries that can feed suggested downstream analyses including multiple sequence alignment and phylogenetic reconstruction.
• Multiple sequence alignment support: Integration with ClustalW and MAFFT for producing multiple sequence alignments from query results.
• Phylogenetic analysis platform: Platform for conducting phylogenetic analyses that can be combined with GECA visualizations to view gene structure in an evolutionary context.
• PeroxiScan family-specific profiles: Updated and expanded family-specific profiles in PeroxiScan that include new sub-families for targeted sequence analysis.

Scientific Applications:

• Comparative genomics: Analysis of gene-structure conservation and intron patterns across peroxidase family members and species.
• Functional annotation: Assignment of putative functions to newly sequenced peroxidase genes using curated sequences, family profiles, and EST-derived evidence.
• Phylogenetic studies: Reconstruction and interpretation of evolutionary relationships among peroxidase sequences using integrated phylogenetic tools and visualizations.

Methodology:

Semi-automatic expert-driven annotation from genomic sequences and EST libraries; genomic cross-referencing of sequences; CIWOG detection of common introns; GECA visualization of gene structure with sequence conservation; PeroxiScan family-specific profile searches; BLAST queries; multiple sequence alignment with ClustalW or MAFFT; and phylogenetic analyses via the integrated platform.