Chetan and Chen Biocomputing Project Submission

bioinformaticsProject/ref_sequences/finalcandidates.txt

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+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

bioinformaticsProject/ref_sequences/finalscript.sh

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+#This script is for the final project of Biocomputing
+#Usage: bash finalscript.sh
+
+#STEP 1a: combine all hsp files in ref_sequences into a total file called HSP_file.fasta
+cat hsp*.fasta >> HSP_file.fasta
+#STEP 1b: combine all mcrA files in ref_sequences into a total file called mcrA_file.fasta
+cat mcrA*.fasta >> mcrA_file.fasta
+
+#STEP 2a: Search for HSP in each proteome
+./muscle -in HSP_file.fasta -out HSP_Muscle.afasta
+#STEP 2b: Search for mcrA in each proteome
+./muscle -in mcrA_file.fasta -out MCRA_Muscle.afasta
+
+#STEP 3a: Build hmm profile
+~/Private/bin/bin/hmmbuild HSP_hmm.txt HSP_Muscle.afasta
+#STEP 3b: Build mcrA profile
+~/Private/bin/bin/hmmbuild MCRA_hmm.txt MCRA_Muscle.afasta
+
+#STEP 4: Count matches for HSP and MCRA (against  each proteome)
+for number in proteome*.fasta
+do
+name=$(echo $number | cut -d_ -f 2| cut -d. -f 1)
+~/Private/bin/bin/hmmsearch --tblout match${name}resultsHSP.search HSP_hmm.txt $number
+~/Private/bin/bin/hmmsearch --tblout match${name}resultsMCRA.search MCRA_hmm.txt $number
+done
+
+#STEP 5: Make table with proteome number in first column, number of HSP matches in second column, and number of MCRA matches in third column
+for i in {01..50}
+do
+coltwo=$(cat match"$i"resultsHSP.search | grep -v "#" | wc -l)
+colthree=$(cat match"$i"resultsMCRA.search | grep -v "#" | wc -l)
+echo "Proteome $i   $coltwo"   "$colthree"
+done
+