PPFINDER is a Perl-based procedure for finding processed pseudogenes in genome annotations (GTF format). PPFINDER identifies pseudogenes using two different methods, and creates a GTF file with pseudogene coordinates that can be used for masking the genome sequence. In gene prediction mode, PPFINDER will mask out the genomic sequence and rerun gene prediction. Rounds of pseudogene masking and gene prediction are iterated until convergence.
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