https://bioinformaticsonline.com/snippets/view/44212/perl-script-to-find-inverted-repeats? https://bioinformaticsonline.com/snippets/view/44212/perl-script-to-find-inverted-repeats Tue, 07 Mar 2023 06:25:23 -0600 https://bioinformaticsonline.com/snippets/view/44212/perl-script-to-find-inverted-repeats #!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $seqio = Bio::SeqIO->new(-file => $genome_file, -format => "fasta"); my $seqobj = $seqio->next_seq(); my $seq = $seqobj->seq(); # run RepeatMasker my $rm = Bio::Tools::Run::RepeatMasker->new(); my $rm_report = $rm->run($genome_file); # parse RepeatMasker output while (my $rm_result = $rm_report->next_result()) { my $rm_match = $rm_result->repeat_consensus(); my $rm_class = $rm_result->repeat_class(); my $rm_start = $rm_result->start(); my $rm_end = $rm_result->end(); my $rm_strand = $rm_result->strand(); if ($rm_class eq "Inverted") { my $rm_seq = substr($seq, $rm_start-1, $rm_end-$rm_start+1); if ($rm_strand eq "-") { $rm_seq = reverse_complement($rm_seq); } print "Inverted repeat found at positions $rm_start-$rm_end: $rm_seq\n"; } } sub reverse_complement { my ($seq) = @_; $seq = reverse($seq); $seq =~ tr/ACGTacgt/TGCAtgca/; return $seq; }]]> BioStar