Wei_Ex11

ex11_2script.sh

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+#Usage: To make this part easier, mv porteFin.fasta ../../InsertFilePath from problem one to the same folder where hammer is.
+./hmmbuild pt1.fasta porteFin.fasta
+
+for file in ./proteosomes/*
+do
+echo $file >> ex11_2_script.txt 
+./hmmsearch --tblout pt2.hits pt1.fasta $file
+cat pt2.hits | grep -v "#" | wc -l >> ex11_2_script.txt
+echo >> ex11_2_script.txt
+done
+

ex11_script.sh

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+#Usage: have gene_sequences in your current directory
+
+for file in ./gene_sequences/*spore*
+do
+	cat $file >> sporFin.fasta
+	echo >> sporFin.fasta
+done
+
+for file in ./gene_sequences/*porter*
+do
+	cat $file >> porteFin.fasta
+	echo >> porteFin.fasta
+done
+
+../../local/bin/muscle3.8.31_i86linux64 -in sporFin.fasta -out sporFin.fasta
+../../local/bin/muscle3.8.31_i86linux64 -in porteFin.fasta -out porteFin.fasta