So far I have a working example although I'm not sure if does exactly what I want it to.

That's what tests are for.

I could use some feed back on this or the whole progam in general.

• autodie to check your open/close/system.
• You open FASTA, but never write to it. Update: tricky... you do write to the file via system. So, there is no need to open the FASTA filehandle.
• perlcritic for other style issues.