You could also wrote this

if(/^>/) {

instead this:

if($_ =~ />/) {

That's a little more precise for your case probably

personally I prefer this more compact form also, but this is a matter of style only

if(/^>/) {$seq = $_} 
else {$accession{$seq} .= $_}
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if you want in any case to write the same like this, I suggest that you consider indent your code

if($_ =~ />/) {
       $seq = $_;
} else {
       $accession{$seq} .= $_;
}
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AND last but not least, don't try to reinvent the wheel, I strongly suggest you to take a look to the bioperl modules, specially the modules related with managing fasta files