Results for "New Genome"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import...1127 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -quer...1093 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse command line...1092 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use...while (my $line = ) { next unless $line =~ /^([ATGCN]+)/; my $genome = $1; my $len_genome = length $genome; my @s...2906 days ago
- ...out URL for the DAS server. Example: # http://genome.ucsc.edu/cgi-bin/das/calJa...t=chr14:482280,483280 my $URL_gene ="http://genome.ucsc.edu/cgi-bin/das/papAnu2/...$xml = get($URL_gene); my $xp = XML::XPath->new(xml=>$xml); my $nodeset = $xp...
2901 days ago
Perl script to generate a random psuedo DNA sequence !
#!/usr/bin/perl print "Enter a number of nucleotides: \n"; chomp ($N = ); @b=qw/A T G C/;print ">Genome\n";while($l2874 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >N...7:H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCA...7:H7 str. EC4115 chromosome, complete genome AGCTTTTCATTCTGACTGCAACGGGCAA...7:H7 str. EC4115 chromosome, complete genome TTAAAA2843 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV...1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -...2618 days ago
Perl script to insert the DNA string in genome
...eq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1];...e of the insertion my $seq_in = Bio::SeqIO->new( -format => 'fasta',-file => $file); my $seq_out = Bio::SeqIO->new( -format => 'fasta',-file => ">"...2650 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Aut...[ -f $MYDB.nhr ] then echo "BLAST database for MergedContigs.fasta genome exists" else echo "Thanks...2643 days ago
