Update: Credited the wrong person.

I'd suggest a slight modification to ww's method. As this is a FASTA file, I'd read the file record by record (sequence by sequence), rather than line by line. The following one-liner ought to work, but is untested. 

perl -e"BEGIN{$/=qq[\n>]}" -wpe"s[[-*]|DL;][]g" theFile > theOuput

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In reply to Re: Substitution on a sequence by BrowserUk
in thread Substitution on a sequence by uvnew

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