bb_reciprocal_blast - ampinzonv/BB3 GitHub Wiki

Function: bb_reciprocal_blast

Perform a reciprocal BLAST between two FASTA files and extract pairs that are mutually best hits (RBH).

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🔍 Description

This function conducts two BLAST searches (A vs B and B vs A), then identifies reciprocal best hits—sequence pairs where each is the best hit for the other. This approach is commonly used to infer orthologous gene pairs between species.

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⚙️ Usage

bb_reciprocal_blast --query FILE --subject FILE --blast_type TYPE [--outfile PREFIX] [--min_identity PCT] [--min_coverage PCT] [--processors N] [--quiet] [--force]

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🧵 Parameters

Option	Description
--query FILE	FASTA file containing the query sequences (required)
--subject FILE	FASTA file containing the subject sequences (required)
--blast_type TYPE	BLAST algorithm to use (blastn, blastp, tblastn, etc.) (required)
--outfile PREFIX	Output prefix for result files (optional)
--min_identity PCT	Minimum percent identity to accept a hit (default: 0)
--min_coverage PCT	Minimum percent coverage of query length (default: 0)
--processors N	Number of CPU threads to use (default: 1)
--quiet	Suppress informational messages
--force	Overwrite output files if they exist

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📤 Output Files

Given the prefix results, the following files will be created:

• results.A_vs_B.blast: BLAST output from A vs B
• results.B_vs_A.blast: BLAST output from B vs A
• results.reciprocal.tsv: List of reciprocal best hit pairs (tab-separated)

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🧪 Example

bb_reciprocal_blast \
  --query genes_A.faa \
  --subject genes_B.faa \
  --blast_type blastp \
  --outfile rbh_output \
  --min_identity 30 \
  --min_coverage 50 \
  --processors 4

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📌 Notes

• Uses bb_blast_on_the_fly for alignment and bb_blast_best_hit for filtering.
• A reciprocal hit is retained only if both hits meet identity and coverage thresholds.
• Coverage is computed using the length of the query sequence (qlen).