Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~Lan787/term4_files/script.txt Дата изменения: Tue Mar 28 03:00:00 2006 Дата индексирования: Tue Oct 2 12:12:50 2012 Кодировка:

rm $2 $3
#------first domains alignment-------
start=(193 4 6 26 26 26) #set start points of domains
end=(631 402 319 413 413 413) #set end points of domains
protein=(AMY1_ECOLI AMY2_ECOLI AMYA_METJA AMYC_HUMAN AMYP_HUMAN AMYS_HUMAN) #set proteins containing domains
i=0
until test $i -eq 6; do
extractseq $1:${protein[i]} -regions ${start[i]}-${end[i]} -auto ${protein[i]}.fasta #get 1st domain to align
j=5
until test $j -eq $i; do
extractseq $1:${protein[j]} -regions ${start[j]}-${end[j]} -auto ${protein[j]}.fasta #get 2nd domain to align
needle ${protein[i]}.fasta ${protein[j]}.fasta -auto alignment.ali #align domains
identity=`awk '($2=="Identity:"){print $4}' grep -v "#" "${protein[i]}-${protein[j]}_1st.txt" #print alignment to file
echo "${protein[i]}-${protein[j]}_1st$identityAlignment"|tr -d "()%">>$2 #print identity to file
rm ${protein[j]}.fasta alignment.ali #rm temp file
((j--)) #decrement variable
done
rm ${protein[i]}.fasta #rm temp file
((i++)) #increment variable
done
#-----second domains alignment-----------
protein=(AMYC_HUMAN AMYP_HUMAN AMYS_HUMAN)
i=0
until test $i -eq 3; do
extractseq $1:${protein[i]} -regions 26-413 -auto ${protein[i]}.fasta
j=2
until test $j -eq $i; do
extractseq $1:${protein[j]} -regions 26-413 -auto ${protein[j]}.fasta
needle ${protein[i]}.fasta ${protein[j]}.fasta -auto alignment.ali
identity=`awk '($2=="Identity:"){print $4}' grep -v "#" "${protein[i]}-${protein[j]}_2nd.txt"
echo "${protein[i]}-${protein[j]}_2nd$identityAlignment"|tr -d "()%" >>$2
rm ${protein[j]}.fasta alignment.ali
((j--))
done
rm ${protein[i]}.fasta
((i++))
done