Collection of scripts to look for the TRGs described in the paper Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels, Sayavedra et al., 2015 and Sayavedra et al., 2019
Looking for toxin-related genes (TRGs) in bacterial genomes is not a straightforward task. The functional domains have often a mosaic-like structure that makes classification a difficult task. To look for TRGs in multiple genomes without the pain of doing it manually, I created a workflow of classification for the follow up paper Comparative genomic inisghts into the roles of toxin-realted genes in the beneficial bacteria and their acquisition by horizontal gene transfer.
The folllowing is the draft of the protocol that was used! The code will be cleaned and updated.
- Blast protein sequences of the genomes you want to look at against the TRG proteins from the Bathy SOX described in [Sayavedra et al., 2015] (https://elifesciences.org/content/4/e07966).
blastp -query Genomes.faa -db ~/ownCloud/ToxinsOtherSOXs/BLAST/bathyt_toxins.faa -max_target_seqs 50 -outfmt "6 std qcovs" -evalue 0.001 -out Genes2Search_vsTRGs.txt
- Use minimum similarity of 25, minimum alignment of 200, minimum coverage of 15
cat Genes2Search_vsTRGs.txt | awk '{if ($3>25 && ($13>25 && $4>50) || ($13>15 && $4>200) ) print $0}' | perl -pe "s/(\S+).*/\1/" | sort -u >Genes2Search_vsTRGs.blastSim25Cov25.txt
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Submit genes from the TRGs paper to the CD-Search Tool, standard settings
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Download results full, include query defline
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Use the list that describes which domains are associated to which class of toxins DomainsClassifier.txt
perl ~/Dropbox/perl_scripts/Findidentifiers_printseq.pl -inident BLAST_possibleToxinsInRelativesIDsSIm25COv50.txt -inseq ~�/ownCloud/ToxinsOtherSOXs/SpeciesTree/fnnGenomes/Genes2Search.faa -o BLAST_possibleToxinsInRelativesSIm25COv50.faa
perl ClassifyTRGs.pl -domains DomainsClassifier.txt -CPD PossibleTRGsSim25Cov50Aln50_hitdata.txt -faa ~/ownCloud/ToxinsOtherSOXs/MassiveClassiffier/BLAST_possibleToxinsInRelativesSIm25COv50.faa.fas -genids GenomeTags.txt -out PossibleTRGsSim25Cov50Aln50