Perl script to find inverted repeats !
...ons $rm_start-$rm_end: $rm_seq\n"; } } sub reverse_complement { my ($seq) = @_; $seq = reverse($seq); $seq =~ tr/ACGTacgt/TGCAtgca/; return $seq; }437 days ago
Perl script to find edit distance between two sequences !
#!/usr/bin/perl use strict; use warnings; sub edit_distance { my ($s1, $s2) = @_; my $len1 = length($s1); my $len2 = length($s2); my @dp; for (my $i = 0; $i436 days ago
Raku script to find palindrome in genomes !
...{ say "Palindrome found at position $pos: $substring"; } } } } # Example usage my $dna = "GGATCCATGGCCTAGG"; # example DNA sequence...436 days ago
4 days ago
Perl script for chi-squared test !
...gs; use Getopt::Long; use FAlite; # sanity checks die "Usage: chidi.pl \n" if (!$ARGV[1]); my @dinucs = qw (AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT); # hash...423 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count = $sequence.comb(//).elems; my $t...otal-bases = $sequence.chars; return $gc-count / $total-bases * 100; } my $dna_sequence = "ATGCGCTAAAGCGCGCGCCTTACGCGCGCGCGC"; my $gc_co...123 days ago
Perl script to calculate GC content !
#!/usr/bin/perl sub calculate_gc_content { my ($sequence) =...the sequence to uppercase my $gc_count = () = $sequence =~ /[G...bases = length($sequence); my $gc_content = ($gc_count / $total...GATCG"; my $gc_content = calculate_gc_content($dna_sequence); prin...108 days ago
Perl script to calculate the basic stats of the assembled genome !
...culate N50 my $n50 = calculate_n50(\@contig_lengths); # Calculate GC content my $gc_content = calculate_gc_conten...return 0; # Should not reach here } # Subroutine to calculate GC content sub calculate_gc_con...106 days ago
Python script for basic stats of the assembled genome !
...ngth in lengths: cumulative_size += length if cumulative_size >= half_size: return length # Calculate GC content def calculate_gc_content(file): gc_count...106 days ago