2695 days ago
Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fasta file (geno...2661 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Author: Jite...@" if [ -f $MYDB.nhr ] then echo "BLAST database for MergedContigs.fasta geno...2654 days ago
Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for geno...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_gen...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_gen...l 'ftp://ftp.ncbi.nlm.nih.gov/geno...2534 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {prin...2533 days ago
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome_gff cd genome_gff # Look...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_gen...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_gen...l 'ftp://ftp.ncbi.nlm.nih.gov/geno...2525 days ago
Calculate Dinucleotide Frequency with Perl
#!/usr/bin/perl -w use strict; my ($genome, $head, $tail); my (%mono_nt, %di_nt); $/ = ">"; open my $fasta, '2340 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstrati...ulation = shift @_; my $pop_size = scalar @$population; # p...in trouble die "Population size $pop_size is too small" if $p...rent_population[int(rand($pop_size))]; my $child = { survived...ref; printf "generation %d: size %dnleast fit DNA [%s]/%d\n...2374 days ago
Clump Finding Problem Solved with Perl
#Find patterns forming clumps in a string. #Given: A string Genome, and integers k, L, and t. #Return: All distinct k-mers forming (L, t)-clumps in Geno...2336 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted by name+location #Geno...2316 days ago