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 (genome...2660 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: Jit..." if [ -f $MYDB.nhr ] then echo "BLAST database for MergedContigs.fasta genome...2653 days ago
Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for geno...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_gen...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_gen...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes...2533 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print...2532 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/genomes...2524 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, '2339 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstration with word DNA (512...arting point my $dna_length = 512; # 4 "letters" in the DNA my $dna_byte_len...} # eliminate words over $max_entry_length letters, and uppercase them @dict...2373 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 Genome....2335 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 #Genomec...2315 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage c...; =head1 NAME psl_scaffolder.pl - use self-mapped PSL file to scaffold a genome...2309 days ago