Results for "genome notes"
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 impor...1119 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 -que...1085 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 #Pars...1085 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use List::Util qw/ shuffle /; my...while (my $line = ) { next unless $line =~ /^([ATGCN]+)/; my $genome = $1; my $len_genom...2898 days ago
- #!/usr/bin/env perl use strict; use warnings; use LWP::Simple; use XML::XPath; us...gure out URL for the DAS server. Example: # http://genome.ucsc.edu/cgi-bin/das/calJac3/...egment=chr14:482280,483280 my $URL_gene ="http://genom...
2893 days ago
Perl script to generate a random psuedo DNA sequence !
#!/usr/bin/perl print "Enter a number of nucleotides: \n"; chomp ($N = ); @b=qw/A T G C/;print ">Genome\n";while($l2866 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCA...7:H7 str. EC4115 chromosome, complete genome AGCTTTTCATTCTGACTGCAACGGGCAA...7:H7 str. EC4115 chromosome, complete genom...2835 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos = $ARGV[1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->...2610 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 (genom...2642 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 genom...2635 days ago
