Final Submission

Marton_Sarah_Madeline.sh

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+# contributors:
+	# Sarah Nicholls
+	# Madeline Laporte
+	# Marton Barta
+
+## Putting all our mcrAgenes and hsp70gene into their own files (with for loop)
+
+	# mcrAgene
+for i in ./ref_sequences/mcr*.fasta
+do
+cat $i >> mcrAgene.fasta
+done
+	# hsp70gene
+for i in ./ref_sequences/hsp*.fasta
+do
+cat $i >> hsp70gene.fasta
+done
+
+## Alligning reference sequences (with muscle)
+
+	# mcrAgene
+./muscle -in mcrAgene.fasta -out MCRA_Muscle.afasta
+
+	# hsp70gene
+./muscle -in hsp70gene.fasta -out HSP_Muscle.afasta
+
+## Building hmm profiles for the  mcrAgene & hsp70gene
+
+	# mcrAgene
+./hmmbuild mcrAgene.hmm MCRA_Muscle.afasta
+
+	# hsp70gene
+./hmmbuild hsp70gene.hmm HSP_Muscle.afasta
+
+
+## initializing the final table
+echo "
+HSP70 & mcrA output
+" > final.tbl
+
+## Searching the proteomes for mcrAgene and hsp70gen (with hmmsearch)
+for genes in ./proteomes/*.fasta
+do
+./hmmsearch --tblout $genes.hsp70gene.tbl hsp70gene.hmm $genes
+./hmmsearch --tblout  $genes.mcrAgene.tbl mcrAgene.hmm $genes
+done
+
+## counting all the times we found gene matches
+for genes in ./proteomes/*.fasta
+do
+x=$(echo $genes | sed -E 's/[^0-9]//g')
+hsp=$(cat $genes.hsp70gene.tbl | grep "HSP_Muscle" | uniq | wc -l)
+mcrA=$(cat $genes.mcrAgene.tbl | grep "MCRA_Muscle" | uniq | wc -l)
+echo "Proteome" $x $hsp "HSP" $mcrA "mcrA" >> final.tbl
+done
+
+## saving all the genes that are considered candidates
+grep -v ' 0 ' final.tbl > candidates.txt
+
+## Thank you :)))
+

README.md

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+# Project from Sarah Nicholls (TA: Tim Burton), Madeline Laporte (TA: Tim Burton), Marton Barta (TA: Ceara J. Talbot)

candidates.txt

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+
+HSP70 & mcrA output
+
+Proteome 03 3 HSP 1 mcrA
+Proteome 05 2 HSP 1 mcrA
+Proteome 07 2 HSP 1 mcrA
+Proteome 15 1 HSP 1 mcrA
+Proteome 16 1 HSP 1 mcrA
+Proteome 19 1 HSP 2 mcrA
+Proteome 23 2 HSP 2 mcrA
+Proteome 24 2 HSP 1 mcrA
+Proteome 38 1 HSP 1 mcrA
+Proteome 39 1 HSP 1 mcrA
+Proteome 42 3 HSP 1 mcrA
+Proteome 44 1 HSP 1 mcrA
+Proteome 45 3 HSP 1 mcrA
+Proteome 48 1 HSP 1 mcrA
+Proteome 50 3 HSP 1 mcrA