diff --git a/EX11Problem1.sh b/EX11Problem1.sh
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index 0000000..d32a910
--- /dev/null
+++ b/EX11Problem1.sh
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+for file in IBC_EX11/gene_sequences/s* 
+do
+	cat $file>> sporecoatTot.fasta #Cats the files for sporecoat 
+	echo \n >> sporecoatTot.fasta #Adds the newline to the end
+done
+for file in IBC_EX11/gene_sequences/t*
+do
+	cat $file>> transporterTot.fasta #Cats the files for transporter
+	echo \n  >> transporterTot.fasta #Adds the new line to the end
+done
+
+./muscle3.8.31_i86linux64 -in sporecoatTot.fasta -out sporecoatTot.align  #creates align for sporecoat
+./muscle3.8.31_i86linux64 -in transporterTot.fasta -out transporterTot.align #Creates align for transporter
+
diff --git a/EX11_Problem2.sh b/EX11_Problem2.sh
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+++ b/EX11_Problem2.sh
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+./local/bin/hmmbuild transporterTot.hmm transporterTot.align  #creates the hmm file
+for file in IBC_EX11/proteomes/*.fasta  #for all the files in proteomes
+do
+./local/bin/hmmsearch --tblout $file.hits transporterTot.hmm $file  #creates a hit file with matches
+echo "Number of hits in $(echo "$file") is $(cat $file.hits| grep -v "#"| wc -l)">>Hits_In_File.txt  #tells the file and number of hits
+done
+