use Seeder::Finder; my $finder = Seeder::Finder->new( seed_width => "6", strand => "revcom", motif_width => "12", n_motif => "10", hd_index_file => "6.index", seq_file => "Potato_FldvsWTinC_INDUCED_gene_list_promoters.faa", bkgd_file => "Potato_genome_promoters.bkgd", out_file => "Potato_FldvsWTinC_INDUCED_gene_list_promoters.faa", ); $finder->find_motifs;