FishMap: a community resource for zebrafish genomics

Abstract

An enormous amount of information on a genomics scale is available for zebrafish (Danio rerio), which is a well-studied model organism for human diseases. However, a majority of this annotation is scattered in obscure data sources. There have been limited efforts to present it on a unified and integrated platform, which would help to understand the biological processes in this organism better. FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. The datasets have been methodically collected from various resources and supplementary information of publications and mapped to the zebrafish genome. The data are organized into nine major sections, which include comparative genomics, mapping and sequencing, gene and gene predictions, expression and regulation, and variation and repeats. A number of unique sections have been incorporated, which include tracks on noncoding gene annotation, location of retrovirus/transposon integrations in the genome, and their flanking genomic sequences and novel transcripts. The datasets are linked to related data sources. FishMap is built on the Gbrowse, which is a part of the Generic Model Organism Database Consortium Project. The resource also features a Web-based BLAST server for sequence homology search and a gene ID converter that would enable users to sift through different interchangeable gene annotation identifier systems. The database is amenable to programmatic access through the Distributed Annotation System as well as BioMoby protocols, thus making it a central community resource that can be integrated with existing data mining and analysis workflows. We hope that FishMap would be an integral resource for community participation in zebrafish genomics. The resource is freely available at http://miracle.igib.res.in/fishmap, or at http://fishmap.igib.res.in.