8/foxp2.pl

#!/usr/bin/perl -w

use strict;

# 1 # Read sequences and store them in a hash

open(IN, 'foxp2.fasta') or die "Could not open file\n";
my %nonhuman;
my $id = undef;
my $seq;
my $id_human;
my $humanseq;
while (<IN>) {
    chomp;
    if (/^>/) {
        if ($id) {
            if ( $id !~ /HUMAN/ ) {
                $nonhuman{$id} = $seq;
            }
            else {
                $humanseq = $seq;
                $id_human  = $id;
            }
        }
        $id = $_;
        $id =~ s/>//;
        $seq = '';
    }
    else {
        $seq .= $_;
    }
}
$nonhuman{$id} = $seq;    # this assumes that we know that the    
                          # final sequence read is non human

close IN;

# 2 # Analyze the multiple alignment

for ( my $i = 0 ; $i < length($humanseq) ; $i++ ) {
    my $unique = 1;
    foreach my $key ( keys %nonhuman ) {

        # check if the amino acid in the human sequence
        # is the same as in the non-human sequence
        if ( substr( $humanseq, $i, 1 ) eq 
             substr( $nonhuman{$key}, $i, 1 ) ) {
              $unique = 0;
        }
    }
    if ($unique) {
	my $pos = $i + 1; 
        print "At position $pos\n";
        my $aa = substr( $humanseq, $i, 1 );
        print "$id_human\t$aa\n";
        foreach my $key ( keys %nonhuman ) {
            my $aa = substr( $nonhuman{$key}, $i, 1 );
            print "$key\t$aa\n";
        }
    }
}