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

my $fasta = << '__FASTA__';
>gi1 cds
ATG fun
>gi2 cds
ATG fun
>gi3 cds
GGG fun
__FASTA__

my @seq_with_hdr = split /\n>/, $fasta;
$seq_with_hdr[0] =~ s/^>//;

my %hdr_by_seq;

for (@seq_with_hdr) {
    my ($hdr, $seq) = split /\n/;
    $hdr_by_seq{$seq} = $hdr;
}

for my $seq (keys %hdr_by_seq) {
    print ">$hdr_by_seq{$seq}\n$seq\n"
}