GEN220 Wk2 protein_seqs

protein_seqs

#!/bin/perl
use strict;

my %seq;
$seq{'AAC35278'} = 'LLIAITYYNEDKVLTARTLHGVMQNPAWQKIVVCLVFDGIDPVLATIGV-VMKKDVDGKE';
$seq{'AnCSMA'} = 'AMCLVTCYSEGEEGIRTTLDSIALTPN-SHKSIVVICDGIIKVLRMMRD-TGSKRHNMAK';
$seq{'AfCHSF'} = 'ALCLVTCYSEGEEGIRTTLDSIAMTPN-SHKTIIVICDGIIKVLRMMRD-TGSKRHNMAK';
$seq{'AAF19527'} = 'AILLVTAYSEGELGIRTTLDSIATTPN-SHKTILVICDGIIKVLGMMKD-RGSKRHNMAK';
$seq{'P30573-1'} = 'TINLVTCYSEDEEGIRITLDSIATTPN-SHKLILVICDGIIKVLDMMSDAQGSKRHNMAK';

my $seq1 = 'AAC35278';
my $seq2 = 'AnCSMA';
my $seq3 = 'AfCHSF';
my $seq4 = 'AAF19527';
my $seq5 = 'P30573-1';

print "$seq1 = $seq{$seq1}\n", "$seq2 = $seq{$seq2}\n", "$seq3 = $seq{$seq3}\n", "$seq4 = $seq{$seq4}\n", "$seq5 = $seq{$seq5}\n";


my $gap = 0;
my $pos = 0;

while ($pos < length($seq{'AAC35278'})) {
my $gap1 = substr($seq{'AAC35278'},$pos,1);
        if ($gap1 eq "-") {
        $gap++;
        }
$pos++;
}

my $gap2 = ($seq{'AnCSMN'}=~ tr/-//);
my $gap3 = ($seq{'AfCHSF'}=~ tr/-//);
my $gap4 = ($seq{'AAF19527'}=~ tr/-//);
my $gap5 = ($seq{'P30573-1'}=~ tr/-//);

print   "The number of gapped columns in $seq1 is $gap\n",
        "The number of gapped columns in $seq2 is $gap2\n";