in reply to miRDeep2 and miRBase
Maybe the Bio::DB::Fasta CPAN modules might be of use to you.
Perhaps providing some sample data would help us help you, including true and not true miRNA sequences.
As well, show us what perl code, if any, you have tried so far.
If this is not a perl-related question, you are looking in the wrong place for help.
Anne
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Seekers of Perl Wisdom