List of string comparison algorithms !
String comparison: Levenshtein Distance Damerau-Levenshtein Distance Jaro Distance Jaro-Winkler Distance Match Rating Approach Comparison Hamming Distance More at https://jellyfish.readthedocs.io/en/latest/comparison.html1009 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
text=" ATGGTV AGTGACCTAGAGTGATGA G GGRTTT" echo "$text" | sed 's/ //g' OR echo "$text" | awk '{ gsub(/ /,""); print }' Return: ATGGTVAGTGACCTAGAGTGATGAGGGRTTT...983 days ago
977 days ago
Split the string with underscore and store values in array with AWK !
more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}' #Other extraction more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}'> enriched_ids_list awk 'NR==FNR{tgts[$1]; next} $1 in tgts' enriched_ids_list result/GO.out > enriched_GO.out.xls921 days ago
Raku script to find palindrome in genomes !
...> $length { for 0..^$dna.chars - $length -> $pos { my $substring = $dna.substr($pos, $lengt...if is-palindrome($substring) { say "Pali...} } # Example usage my $dna = "GGATCCATGGCCTAGG"; # example...451 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count = $sequence.comb(//).elems...return $gc-count / $total-bases * 100; } my $dna_sequence = "ATGCGCTAAAGCGCGCG...GCGCGCGCGC"; my $gc_content = calculate-gc-content($dna_se...139 days ago
121 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 $gff_file = 'path/to/your/file.g...121 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): r...len(sequence) - min_repeat_length + 1): substring = sequence[i:i+min_repeat_length] if sequence.count(substring) > 1 and substring not in rep...121 days ago
Raku script to find microsatellites in DNA fragments !
sub find-microsatellites($sequence, $min-repeat-length...$min-repeat-count + 1) -> $i { my $substring = $sequence.substr($i, $repea...t-length); if $sequence.contains($substring x $min-repeat-count) {...121 days ago