echo Please enter coordinates of the first domen from TYPH_ECOLI now
seqret sw:P07650 -sask
echo Please enter coordinates of the first domen from TYPH_METJA now
seqret sw:Q58081 -sask
echo Please enter coordinates of the first domen from TYPH_HUMAN now
seqret sw:P19971 -sask
 
echo Please enter coordinates of the second domen from TYPH_ECOLI and save results in file "typh_ecoli1.fasta"
seqret sw:P07650 -sask
echo Please enter coordinates of the second domen from TYPH_METJA and save results in file "typh_metja1.fasta" 
seqret sw:Q58081 -sask
echo Please enter coordinates of the second domen from TYPH_HUMAN and save results in file "typh_human1.fasta"
seqret sw:P19971 -sask 


echo Please enter coordinates of the third domen from TYPH_ECOLI and save results in file "typh_ecoli2.fasta"
seqret sw:P07650 -sask 
echo Please enter coordinates of the third domen from TYPH_METJA and save results in file "typh_metja2.fasta"
seqret sw:Q58081 -sask
echo Please enter coordinates of the third domen from TYPH_HUMAN and save results in file "typh_human2.fasta" 
seqret sw:P19971 -sask 


cat typh_ecoli.fasta > PF02885.fasta
cat typh_metja.fasta >> PF02885.fasta
cat typh_human.fasta >> PF02885.fasta

cat typh_ecoli1.fasta > PF00591.fasta
cat typh_metja1.fasta >> PF00591.fasta
cat typh_human1.fasta >> PF00591.fasta

cat typh_ecoli2.fasta > PF07831.fasta
cat typh_metja2.fasta >> PF07831.fasta
cat typh_human2.fasta >> PF07831.fasta

emma PF02885.fasta PF02885.aln -auto
emma PF00591.fasta PF00591.aln -auto
emma PF07831.fasta PF07831.aln -auto