Download the genome from NCBI using bash script/command
...fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembl...| sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\...lant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembl...| sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\...2528 days ago
Download the gff files from NCBI using bash script/command
...fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembl...| sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\...lant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembl...| sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\...2519 days ago
Genetic Algorithms demonstration with word DNA in Perl
...the population my $popsize = 1024; # a good starting point my $dna_len...y written by Abigail # Documentation for the algorithm is at # http://theoryx5...dna = shift @_; my $byte = shift @_; # print "Got byte $byte\n"; my $letter...2368 days ago
Fill up the form and blast with perl
...TCTCAGAGATCTCGATATATTATA'; $mech->get('http://www.arabidopsis.org/Blast/'); $mech->submit_form( form_name => 'myForm', fields => { 'Algorithm' => 'blastx', 'Blas...2322 days ago
Create genome scaffolding with Perl
...quences into memory..."); open(my $queryFile, "=21 tab-separated values, got %d)",...min($sLen - $sEnd, $lLen - $lEnd); ## Only continue on if there's a good likelihood that this will w...2305 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2259 days ago
Plot custom gene density with R
library(karyoploteR) pp2246 days ago
Perl script to find coding regions in DNA sequences
...ar $seq my $i=0; while ($i < scalar(@seql)) { chomp($seql[$i]); $seq = $seq . $seql[$i]; $i = $i + 1; } $seq = "\U$seq"; # we are going to use the array @codons t...2151 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...ttps://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping...2120 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 he...2137 days ago