Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:config auto_version auto_he...2317 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, load it, # if not, install and load it if("ggplot2" %i...2293 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
...; { local $/=">"; while() { chomp; next unless /\w/; s/>$//gs; my @chunk = split /\n/; my $header = shift @chunk; my $...2260 days ago
Plot custom gene density with R
library(karyoploteR) pp2259 days ago
Perl script to read multi fasta sequence one by one
...ie "couldn't open the file $outfile $!"; print OUT "$key\n$fastaSeq{$key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppos...2230 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2163 days ago
Perl script to find coding regions in DNA sequences
...esequence can not be opened\n"; exit(1); } # FASTA format: # >header containing a description of t...AGACTGACTTAC # AGACTGACTTAC # AGACTGAC my $iden = ; # reading the header of the sequence my @seql = ;...2164 days ago
2160 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2153 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here...2149 days ago