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+# This script is for Question 1 of EX11
+# Usage: bash Q1.sh
+
+cat gene_sequences/sporecoat01.fasta > gene_sequences/sp.fasta
+for sp in gene_sequences/sporecoat0[234].fasta
+do
+	echo \n >> gene_sequences/sp.fasta
+	cat $sp >> gene_sequences/sp.fasta
+done 
+./bin/muscle -in gene_sequences/sp.fasta -out gene_sequences/sp.align
+
+cat gene_sequences/transporter01.fasta > gene_sequences/tr.fasta
+for tr in gene_sequences/transporter0[234].fasta
+do
+  	echo \n >> gene_sequences/tr.fasta
+        cat $tr >> gene_sequences/tr.fasta
+done
+./bin/muscle -in gene_sequences/tr.fasta -out gene_sequences/tr.align
diff --git a/Q2.sh b/Q2.sh
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+# This script is for Question 2 of EX11
+# Usage: bash Q2.sh
+
+# build a HMM profile for the transporter gene
+./bin/hmmbuild proteomes/tr.hmm gene_sequences/tr.align
+
+# search the hits to HMM profile
+for bp in proteomes/*.fasta
+do
+	./bin/hmmsearch --tblout ${bp%.*}.hits proteomes/tr.hmm $bp
+done
+
+# count for number of hits
+echo "Number of hits to the HMM profile in each proteome:" > proteomes/hit_counts.txt
+for hits in proteomes/*.hits
+do
+	echo ${hits##*/} >> proteomes/hit_counts.txt
+	cat $hits | grep -v "#" | wc -l >> proteomes/hit_counts.txt
+done
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