In your script, the >456 header is missing before the second sequence. Here's how I would solve your task without BioPerl: 
#!/usr/bin/perl
use warnings;
use strict;

my @contigfile = qw( >37 ABC DEF GHI >456 JKL MNO PQR STU VWX YZ >38 )
+;

my @result;
for my $i (0 .. $#contigfile) {
    my $current = $contigfile[$i];
    push @result, q() and next if 0 == index $current, '>';
    $result[-1] .= $current;
}

print "$_\n" for @result;

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لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Uninitialized value in substr command by choroba
in thread Uninitialized value in substr command by lmtaylor

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