Streff

exercise1.sh

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+#To create file to align sporecoat files, first create sporecoatcombined.fasta by doing cat sporecoat01.fasta sporecoat02.fasta sporecoat03.fasta sporecoat04.fasta > sporecoatcombined.fasta and edit it so no sequence line containes >
+#To create spore coat alignment
+/afs/nd.edu/user5/hstreff/local/bin/muscle3.8.31_i86linux64 -in sporecoatcombined.fasta -out sporecoatalignment.align
+#To create file to align transporter files, first create transportercombined.fasta by doing cat transporter01.fasta transporter02.fasta transporter03.fasta transporter04.fasta > transportercombined.fasta
+#To create transporter alignment
+/afs/nd.edu/user5/hstreff/local/bin/muscle3.8.31_i86linux64 -in transportercombined.fasta -out transporteralignment.align
+

exercise2.sh

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+#To run use bash exercise2.sh
+#Make transporteralignment.align into transporteralignment.hmm
+/afs/nd.edu/user5/hstreff/local/bin/hmmbuiansporteralignment.hmm transporteralignment.align
+#Determine number of hits with Arthrobacter
+echo "transporterArthrobacter.hits" > transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterArthrobacter.hits transporteralignment.hmm Arthrobacter.fasta
+cat transporterArthrobacter.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Bacillus
+echo "transporterBacillus.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterBacillus.hits transporteralignment.hmm Bacillus.fasta
+cat transporterBacillus.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Clostridium
+echo "transporterClostridium.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterClostridium.hits transporteralignment.hmm Clostridium.fasta
+cat transporterClostridium.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Flavobacterium
+echo "transporterFlavobacterium.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterFlavobacterium.hits transporteralignment.hmm Flavobacterium.fasta
+cat transporterFlavobacterium.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Limnohabitans
+echo "transporterLimnohabitans.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterLimnohabitans.hits transporteralignment.hmm Limnohabitans.fasta
+cat transporterLimnohabitans.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Rhizobium
+echo "transporterRhizobium.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterRhizobium.hits transporteralignment.hmm Rhizobium.fasta
+cat transporterRhizobium.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Roseobacter
+echo "transporterRoseobacter.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterRoseobacter.hits transporteralignment.hmm Roseobacter.fasta
+cat transporterRoseobacter.hits | grep -v "#" | wc -l >> transporterhits.txt
+#Determine number of hits with Verrucomicrobia
+echo "transporterVerrucomicrobia.hits" >> transporterhits.txt
+/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterVerrucomicrobia.hits transporteralignment.hmm Verrucomicrobia.fasta
+cat transporterVerrucomicrobia.hits | grep -v "#" | wc -l >> transporterhits.txt

transporterhits.txt

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+transporterArthrobacter.hits
+0
+transporterBacillus.hits
+1
+transporterClostridium.hits
+0
+transporterFlavobacterium.hits
+1
+transporterLimnohabitans.hits
+1
+transporterRhizobium.hits
+0
+transporterRoseobacter.hits
+1
+transporterVerrucomicrobia.hits
+0