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Perl script for six frame translation !
By LEGE 329 days ago
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
# Path to your input nucleotide sequence file in FASTA format
my $input_fasta = 'path/to/your/input.fasta';
# Step 1: Read the input FASTA file
my $seqio = Bio::SeqIO->new(-file => $input_fasta, -format => 'fasta');
my $sequence = $seqio->next_seq;
# Step 2: Perform six-frame translation
my @frames = (1, 2, 3, -1, -2, -3);
foreach my $frame (@frames) {
my $translated_seq = translate_frame($sequence, $frame);
my $frame_type = $frame > 0 ? "Forward" : "Reverse";
print "Frame $frame_type $frame Translation:\n$translated_seq\n";
}
# Subroutine to translate a sequence in a specific frame
sub translate_frame {
my ($sequence, $frame) = @_;
my $translated_seq;
if ($frame > 0) {
$translated_seq = $sequence->translate(-frame => $frame)->seq;
} else {
# If frame is negative, reverse and complement the sequence before translation
my $revcomp_seq = $sequence->revcom;
$translated_seq = $revcomp_seq->translate(-frame => abs($frame))->seq;
}
return $translated_seq;
}
