blast_rbh

blast_rbh performs reciprocal BLAST searches between pairs of sequence files to identify reciprocal best hits for comparative sequence and orthology analyses.

Key Features:

• Reciprocal Best Hits Extraction: Performs two-way BLAST comparisons to identify sequences that are best hits in both directions between two datasets.
• NCBI BLAST+ Integration: Leverages enhancements from the NCBI BLAST+ suite, including rewritten BLAST components, to support improved search behavior.
• Optimized Performance: Segments long query sequences into chunks and retrieves only relevant portions of lengthy database sequences to reduce CPU time and memory usage.
• Galaxy Integration: Can be wrapped within the Galaxy platform to execute BLAST tasks as part of Galaxy workflows.
• Modular Software Library: Uses a modular library to enable access to subject sequence data from various sources.

Scientific Applications:

• Genome Annotation: Identifies reciprocal best hits to support annotation of homologous sequences across species or strains.
• Pan-genome Analyses: Handles extensive sequence datasets to support comparative genomics and pan-genome studies.
• Sequence Verification: Confirms sequence identity in contexts such as verification of capillary sequencing results from single PCR products.

Methodology:

Conducts reciprocal two-way BLAST searches between sequence datasets using NCBI BLAST+, segments long queries into chunks, retrieves relevant portions of lengthy database sequences, and identifies reciprocal best hits.