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Magana submission #12

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Magana submission #12

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1d0c70f
Added file for problem 1
a-magana2 Nov 28, 2018
c0ea370
Added file for problem 2
a-magana2 Nov 28, 2018
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14 changes: 14 additions & 0 deletions EX11Problem1.sh
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Original file line number Diff line number Diff line change
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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

7 changes: 7 additions & 0 deletions 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