Results for "Exploring Gene Networks"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org...len(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-reg...1136 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cannot...GANISM\s*)(.*)/) { print "Organism: $2\n"; } elsif(/(gene)(\s*)(\d*)(\.\.)(\d*)/) { print "Gene len...2917 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::Esc...2916 days ago
- #!usr/bin/perl use strict; use warnings; my %id2seq = (); my $id = 0; open F,"$ARGV[0]...@val = split /\s+/, $_; my @newval=@val; shift @newval; print ">$id [ gene=$va...
2513 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, lo...rary(ggplot2) } # import a text file with gene positions # columns should b...chr, position (no end or gene name required) genes...2284 days ago
Plot custom gene density with R
library(karyoploteR) pp2250 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Seq...>$ARGV[2].cdna.fasta" ); my $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].gene.fasta" ); my $outfile_upstre...the stop codon) # gene - the entire gene seq...2139 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine docker...Manage the docker engine image Manage images network Manage networks node Manage Swarm n...1513 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Download...sage table derived from highly‐expressed A. gambiae genes is appended below. Biote...he human genome reveals that about sixty percent of genes ar...1511 days ago
- jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker sys...will remove: - all stopped containers - all networks not used by at least one...p Profile: default Kernel Version: 4.15.0-88-generic Operating System: Ubuntu 18....
1509 days ago
