PeterMulhair / ChemosGeneAnnotation

Pipeline to annotate chemosensory related genes in insects

ChemosGeneAnnotation

Set of scripts to identify chemsensory related genes in unannotated genomes. Using raw data from 55 lepidopteran and dipteran species, this pipeline can be run iteratively for annotation and confirmation of genes involved in chemosensation in insects. It uses previously identified protein sequences for odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), odorant-binding proteins (OBPs), chemosensory proteins (CSPs) and sensory neuron membrane proteins (SNMPs).

Requirements

• python3
• BLAST+ suite - install for command line
• Exonerate - install
• Pfam for command line

Usage

ChemosGeneAnnotation is a collection of python scripts that is currently run with a string of commands.

Download this repo locally using git clone https://github.com/PeterMulhair/ChemosGeneAnnotation.git

Step 1: Run initial broad tBLASTn search

python blast_run.py --path </path/to/genome/assemblies/> --input raw/chemo_genes.fa --threads <integer>

python parse_blast.py --path </path/to/genome/assemblies/> --taxa results/blastout/

Step 2: Run exonerate on blast ouput

python exonerate_run.py --input raw/

Step 3: Run pfam annotation on exonerate output

python pfam_run.py

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This pipeline can be run as outlined above as many times as required to ensure annotation of all chemosensory genes in your genomes. All you need to do is change the input files to include your newly identified genes.