Although this is not a perl answer, but is good to point when doing bioinformatics and have *nix.

Emboss has a lot of commands to handle sequences (eg. for searching dreg or preg and fuzz*). Also for example blast and interproscan can be downloaded and used locally. And as Itatsumaki said, Bioperl can help out a lot.

In reply to Re: Refomating a large fasta file... by Hena
in thread Refomating a large fasta file... by bioinformatics

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