The catfish genome database (cBARBEL)

The catfish genome database (cBARBEL) provides integrated genetic and genomic data and analysis tools to support genome biology research in ictalurid catfish (Ictalurus spp.).

Key Features:

• Search Functions: BLAST-based searches, fuzzy matching, and specific query support for locating sequences and associated annotations and data.
• Map Visualization: Visualization of linkage maps, physical maps, and integrated maps of catfish genomes.
• EST Contig Viewer with SNP Overlay: Exploration of expressed sequence tag (EST) contigs with single nucleotide polymorphism (SNP) data overlaid.
• GBrowse-based Organization: Genomic data organized and browsed using GBrowse with sequence annotation based on similarity to zebrafish chromosomes.
• Data Integration: Integration of diverse genetic and genomic data resources for combined analysis.

Scientific Applications:

• QTL Mapping: Support for quantitative trait loci (QTL) projects through integrated genomic data for marker localization and candidate gene identification.
• Gene Expression and Variation Studies: Analysis of EST contigs and SNP overlays to study gene expression and genetic variation.
• Comparative Genomics: Comparative analysis by mapping catfish sequences to zebrafish chromosomes to infer conserved regions and synteny.
• Breeding and Genetic Improvement: Support for marker-assisted selection and genetic improvement efforts in catfish breeding programs.

Methodology:

Implements BLAST-based sequence searches and fuzzy matching, GBrowse for genome organization, EST contig viewing with SNP overlay, mapping of sequences by similarity to zebrafish chromosomes, and visualization of linkage, physical, and integrated maps.