Results for "V gene"
Bio-Scripts
Python script to download covid genome !
...seqs = seqs['genbank-sequences'] print("got %d sequences" % len(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-region'] == "complete":...1151 days ago
Parse a genbank file using regular expressions
...print "Sequence name: $2\n"; } elsif (/(ORGANISM\s*)(.*)/) { print "Organism: $2\n"; } elsif(/(gene)(\s*)(\d*)(\.\.)(\d*)/) { print "Gene length: $5\n"; } elsi...2931 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::E...2930 days ago
- ...p; if($_ =~ /^>(.+)/){ $id++; s/\[//g; s/\]//g; my @val = split /\s+/, $_; my @newval=@val; shift @newval; print ">$id [ gene=$val[0] ] [ protein=@newval ]...
2527 days ago
Plot the density of genes in R
...mosome name and column2 = start position of the gene # check if ggplot2 is inst...ibrary(ggplot2) } # import a text file with gene positions # columns should b...: chr, position (no end or gene name required) genes...2299 days ago
Plot custom gene density with R
library(karyoploteR) pp2264 days ago
Perl script to convert GFF 2 FASTA !
...-file => ">$ARGV[2].cdna.fasta" ); my $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].gene.fasta" ); my $outfile_upstre...des a * as the stop codon) # gene - the entire gene sequence (including UTRs and...2153 days ago
Pack a perl program with their dependencies on Ubuntu !
...ae. The input codon usage table derived from highly‐expressed A. gambiae genes is appended below. Biote...uit fly genome with the human genome reveals that about sixty percent of genes are conserved (Adams et al....1526 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified...ASN_BINARY/ 03/07/2020, 07:49:00 GENE_INFO/ 03/07/2020, 07:48:00...0:00 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz ftp://ftp.nc...med.gz ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz ftp://ft...1417 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions fr...ic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedto...1380 days ago
