Perl script to convert Multi-line Fasta to Single-line Fasta !
#!/usr/bin/perl use strict; use warnings; sub multi_to_single_line_fast...tput_filename': $!"; my $current_sequence = ""; while (my $line...# If a header line, write the previous sequence...current sequence $current_sequence ....153 days ago
152 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.gff...152 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my $input...asta, -format => 'fasta'); my $sequence = $seqio->next_seq; # Step...anslated_seq = translate_frame($sequence,...ive, reverse and complement the sequence b...152 days ago
Python script for six frame translation of sequences !
from Bio import SeqIO from Bio.Seq import Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate() else:...r record in records: print(f"Sequence...} {abs(frame)} Translation:\n{protein_sequence}\...152 days ago
Raku script to find repeats in sequences !
sub find-repeats($sequence, $min-repeat-length = 3) { my @repeats; for ^($sequence.chars - $min-repeat-length + 1) -> $i { my $substring = $sequence....n @repeats; } # Example usage my $genome-sequence =...152 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): repeats = [] for i in range(len(sequence) - min_repeat_length + 1): substring = sequence[i:i+min_repeat_length]...return repeats # Example usage genome_sequence =...152 days ago
Raku script to find microsatellites in DNA fragments !
sub find-microsatellites($sequence, $min-repeat-length = 2, $max-repeat-length.....$max-repeat-length) { for ^($sequence.chars - $repeat-length * $min...) -> $i { my $substring = $sequence....@result = find-microsatellites($genome-sequence);...152 days ago
Perl script to parse blast results and plot basic stats !
#!/usr/bin/perl use strict; use warnings; use List::Util qw(sum); # Usage: ....entry->{PERCENT_IDENTITY}, "\n"; print "Alignment Length: ", $entry->{ALIGNMENT_LENGTH}, "\n"; print "E-...: $avg_percent_identity\n"; print "Average Alignment...152 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing the ge...tal_length = 0; my $num_contigs = 0; my @contig_lengths; # Iterate through each sequence i...152 days ago