Homolog Identification Scripts

homolog_identify.sh

The homolog_identify.sh script performs the following tasks:

1. Uses BLAST to search a query file against a subject file.
2. Identifies putative homologs based on:
   • Percent identity greater than 30%.
   • Length of the aligned region being at least 90% of the query length.
3. Processes BLAST results and compares them to a BED file to determine if the putative homologs are located within (boundaries inclusive) gene boundaries.
4. Saves the names of genes with homologs into a .txt file.

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run_homolog_identify.sh

The run_homolog_identify.sh script automates the homolog identification process by:

1. Iterating through a directory containing .faa and .bed files.
2. Running the homolog_identify.sh script for each corresponding pair of .faa and .bed files.

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Other Details

Parameters

• pident: Percent identical matches.
• length: Length of the aligned region between the query and subject.
• query: The query sequence being searched against the database.
• sseqid: The FASTA header in the subject file.

Miscellaneous

• Use the flag -task blastn-short if the query sequence is shorter than 50 bases.