Perillo

Exercise11part1.sh

@@ -0,0 +1,22 @@
+#First, move all sporecoat fasta files from laptop to remote computer using scp.
+
+#Then, cat all sporecoat fasta files into a single file
+cat sporecoat01.fasta sporecoat02.fasta sporecoat03.fasta sporecoat04.fasta > sporecoatmerged.fasta
+
+#Remove '>' using sed and then manually add the first one back in using nano
+sed 's/>//g' sporecoatmerged.fasta > sporecoatalignment.fasta
+
+#Next, run muscle command to generate align file and get alignment
+muscle3.8.31_i86linux64 -in sporecoatalignment.fasta -out sporecoataligned.align
+
+#The next part is quite similar, as we move all transporter files to remote computer using scp
+
+#Then create final fasta file
+cat transporter01.fasta transporter02.fasta transporter03.fasta transporter04.fasta > transportermerged.fasta
+
+#Remove all '>' and then manually add one to the first line using nano
+sed 's/>//g' transportermerged.fasta > transporterfinal.fasta
+
+#Lastly, use muscle
+muscle3.8.31_i86linux64 -in transporterfinal.fasta -out transporteraligned.align
+

Exercise11part2.sh

@@ -0,0 +1,27 @@
+#Build HMM profile for transporter genes using transporterfinal.align
+hmmbuild transporterfinal.hmm transporteraligned.align
+
+#Search in HMM for each species
+hmmsearch --tblout transArthrobacter.hits transporterfinal.hmm Arthrobacter.fasta
+cat transArthrobacter.hits | grep -v "#" | wc -l > transBachits.txt
+
+hmmsearch --tblout transBacillus.hits transporterfinal.hmm Bacillus.fasta
+cat transBacillus.hits | grep -v "#" | wc -l >> transBachits.txt
+
+hmmsearch --tblout transClostridium.hits transporterfinal.hmm Clostridium.fasta
+cat transClostridium.hits | grep -v "#" | wc -l >> transBachits.txt
+
+hmmsearch --tblout transFlavobacterium.hits transporterfinal.hmm Flavobacterium.fasta
+cat transFlavobacterium.hits | grep -v "#" | wc -l >> transBachits.txt
+
+hmmsearch --tblout transLimnohabitans.hits transporterfinal.hmm Limnohabitans.fasta
+cat transLimnohabitans.hits | grep -v "#" | wc -l >> transBachits.txt
+
+hmmsearch --tblout transRhizobium.hits transporterfinal.hmm Rhizobium.fasta
+cat transRhizobium.hits | grep -v "#" | wc -l >> transBachits.txt
+
+hmmsearch --tblout transRoseobacter.hits transporterfinal.hmm Roseobacter.fasta
+cat transRoseobacter.hits | grep -v "#" | wc -l >> transBachits.txt
+
+hmmsearch --tblout transVerrucomicrobia.hits transporterfinal.hmm Verrucomicrobia.fasta
+cat transVerrucomicrobia.hits | grep -v "#" | wc -l >> transBachits.txt

Exercise11part2hits.sh

@@ -0,0 +1,11 @@
+#Concatenate file transBachits.txt to see the outputs
+cat transBachits.txt
+0
+1
+0
+0
+0
+0
+0
+0
+