#!/usr/bin/perl -w 

print "Please type the file name of the protein sequence data: "; 

$proteinfilename = <STDIN>; 

unless ( open (PROTEINFILE, $proteinfilename) ) { 

print "File \"$proteinfilename\" doesn\'t seem to exist!!\n"; 

} 
$protein = <PROTEINFILE> ; 

$empty = " " , (<PROTEINFILE>); 

while ( $protein = <PROTEINFILE> ) { 

if ( $protein =~ /^>/ ) { 

next $protein; 

} else { 

$protein =~ s/$empty//g ; 

$protein = join ($protein, @protein); 

print $protein; 

} 

}