BOSS jr. Documentation

Author: Gurpinder

Last update: 18-12-2024

Overview

Brassica Orthologue Search Script BOSS jr. is a Python script designed for gene mapping between different genomic assemblies, specifically for limited sets of genes (a few hundred at most). It was originally created to find gene mappings between Brassica napus assemblies and orthologues between Arabidopsis and Brassicas. The script performs reciprocal BLAST searches to establish gene correspondences. The script runs blastn, so is suitable for search using CDS sequences.

Dependencies

It has been tested with

• python=3.11
• ncbi-blast=2.12
• Biopython=1.80

Command-Line Interface (CLI):

Boss_jr.py [-h] [--evalue_threshold EVALUE_THRESHOLD] input_file query_database target_database {oto,otm}

Positional Arguments:

input_file: Path to the file containing the list of query gene IDs (one per line).

query_database: Path to the query database (Nucleotide database created using `makeblastdb').

target_database: Path to the target database (Nucleotide database created using `makeblastdb').

flag: Specifies the operation mode:

oto (One-to-One reciprocal BLAST)

otm (One-to-Many reciprocal BLAST)

Optional Arguments:

--evalue_threshold (default: 1e-50): The E-value threshold for filtering BLAST results.

Example:

python boss_jr.py genes.txt query_db.fasta target_db.fasta oto --evalue_threshold 1e-30

Notes

• The script prints the mapping results to the console in a structured format, indicating whether each query gene has a valid mapping in the target database.

• The script is inefficient for large-scale analyses due to the use of Python dictionaries and loops.

• For large-scale gene mappings, consider using pandas for improved performance.