Results for "Gene phylogenies"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.or...en(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-region...1129 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "canno...ANISM\s*)(.*)/) { print "Organism: $2\n"; } elsif(/(gene)(\s*)(\d*)(\.\.)(\d*)/) { print "Gene length...2910 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::Esca...2909 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=$val[0...
2506 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, lo...rary(ggplot2) } # import a text file with gene positions # columns should b...chr, position (no end or gene name required) genes...2278 days ago
Plot custom gene density with R
library(karyoploteR) pp2243 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Seq...>$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 sequen...2132 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:~/Downloa...age table derived from highly‐expressed A. gambiae genes is appended below. Biote...e human genome reveals that about sixty percent of genes are c...1505 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIV...0 ASN_BINARY/ 03/07/2020, 07:49:00 GENE_INFO/ 03/07/2020, 07:48:00...5:30:00 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz ftp://ftp.nc...pubmed.gz ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/g...1396 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic...ronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {prin...1359 days ago
