Elias_Issa-Project1 #8
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qtran4
reviewed
Oct 21, 2022
| #Compiles all the individual hsp70 and mcrA sequences into one file | ||
| cat ref_sequences/hsp70*.fasta > hsp70seq.fasta | ||
| cat ref_sequences/mcrA*.fasta > mcrAseq.fasta | ||
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qtran4
reviewed
Oct 21, 2022
| #Uses combined seq files to form alignments using muscle | ||
| ~/Private/Biocomputing2022/Tools/muscle -in hsp70seq.fasta -out hsp70align.afa | ||
| ~/Private/Biocomputing2022/Tools/muscle -in mcrAseq.fasta -out mcrAalign.afa | ||
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qtran4
reviewed
Oct 21, 2022
| #Uses alignments to build a profile with hmmbuild | ||
| ~/Private/Biocomputing2022/Tools/hmmbuild hsp70profile.hmm hsp70align.afa | ||
| ~/Private/Biocomputing2022/Tools/hmmbuild mcrAprofile.hmm mcrAalign.afa | ||
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qtran4
reviewed
Oct 21, 2022
| #Appends proteome name and hsp70 and mcrA matches to summary file | ||
| echo $a, $b, $c >> summary.csv | ||
| done | ||
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qtran4
reviewed
Oct 21, 2022
| #Removes heading of summary file as well as proteomes with no matches | ||
| #Sorts by number of hsp70 matches (highest to lowest), gets top four matches (each with 3 hsp70) and saves proteome names to candidate file | ||
| cat summary.csv | sed '1d' | sed -e '/, 0/d'| sort -k2,2nr | head -n 4 | cut -d, -f 1 > candidates.txt | ||
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-code efficiency [2 points]
qtran4
reviewed
Oct 21, 2022
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