#!/usr/bin/perl
use strict;
use warnings;

my $data2 = <<D2;
A5V
A5S
...
I152T
D2

my $data1 = <<D1;
>gi|134611|sp|P00441.2|_Homo_sapiens ...
END
D1

my $data1Name = \$data1;
open my $inFile, '<', $data1Name or die "Failed at opening $data1Name: $!\n";

...