#!/usr/bin/perl use strict; use warnings; local $/; # Slurp my $content = ; my ($header) = $content =~ /^(>.*?)$/m; while ($content =~ /^[\w]+?([VMFWLCA]{8,})[\w]+?$/mg) { my $sequence = $1; print $header, "contains $sequence at position ", pos($content) - length($sequence), "\n"; } __DATA__ >P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 | Name=HLA-A; Synonyms=HLAA;M MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDT QFVRFDSDAASQRMEPRAPWIEQEGPEYWDRNTRNVKAHSQTDRANLGTLRGYYNQSEDGS TIQRMYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKW ETAHEAEQWRAYLEGRCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATL RCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWASVVVPSGQEQ RYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVIAGAVVAAVMWRRKS SDRKGGSYSQAASSDSAQGSDMSLTACKV