Blast2Fish

Blast2Fish performs reference-based annotation of transcriptome data from non-model teleost fish to assign homologous sequence matches, Gene Ontology terms, and literature-derived biological annotations for downstream functional enrichment analysis.

Key Features:

• Reference-Based Annotation: Annotates assembled transcriptome sequences using a reference-based homology strategy rather than relying on per-gene pre-defined tags.
• Integration with BLAST and Gene Ontology: Uses the Basic Local Alignment Search Tool (BLAST) together with Gene Ontology analysis to identify homologous sequences and describe sequence characteristics.
• PubMed Article Mining: Retrieves related PubMed articles based on the 500 top BLAST hits and parses biological terms from those articles to include as annotations.
• Functional Enrichment Analysis: Performs functional enrichment analyses to identify enriched GO terms and biological themes, with emphasis on immunology-related topics in non-model teleost fish.

Scientific Applications:

• Transcriptome annotation for non-model teleosts: Enables functional annotation of transcriptomes from teleost species that lack comprehensive genomic resources.
• De novo sequencing projects in commercially important fish species: Supports annotation of sequences generated by de novo transcriptome assemblies in commercially important fish.
• Immunology research: Facilitates investigation of immune-related genes and pathways in teleost fish through GO and literature-augmented annotations.
• Ecology and evolutionary biology: Supports studies of biological processes and evolutionary relationships by providing functional assignments for transcripts.

Methodology:

Performs BLAST searches to identify homologous sequences, applies Gene Ontology analysis, retrieves PubMed articles for the top 500 BLAST hits, and parses and sorts biological terms from those articles to record as annotations.