Script to rapid genome clustering based on pairwise ANI
...n' -max_target_seqs 10000 -o -num_threads 32 Note: using the -perc_identity flag will speed up the sea...tn -query -db -outfmt '6 std qlen slen' -max_target_seqs 10000 -perc_identity 90 -o -num_threads 32...699 days ago
656 days ago
Perl script to read the next line of a file !
my $line = ; while(1) { # keep looping until I say so my $nextLine = ; if ($line =~ m/>/ || !defined $nextLine) { ### Do the stuff } ### Do any other stuff; last unless defined $nextLine; $line = $nextLine; }629 days ago
Identify genome-wide synteny with LASTZ alignment
...his is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ ali...F.fa FFChr1.txt Step2: Alignment using LASTZ and Chain/Net...tnet chr1.chain.filter.qnet netSyntenic chr1.chain.filter.tnet ch...yntenic markers perl Maf2rawsynteny.pl chr1.chain.filter.tnet....581 days ago
Perl script to find inverted repeats !
...$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 pos...489 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; $i488 days ago
Raku script to find palindrome in genomes !
...; # convert to uppercase $str.=subst:g/\s+//; # remove any spaces return $str eq $str.flip; } sub find-palindromes(Str $dna, Int $min-length, Int $max-length) { for $min-...488 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data482 days ago
56 days ago
Perl script for chi-squared test !
...Alite(\*FILE); # loop through each sequence in file 1 while(my $entry = $fasta->nextEntry) { my $seq = uc($entry->...########################################## # need total of all counts in both sequences, plus tota...475 days ago