Results for "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":...1126 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: $5\n"; } elsi...2907 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::E...2906 days ago
- ...p; if($_ =~ /^>(.+)/){ $id++; s/\[//g; s/\]//g; my @val = split /\s+/, $_; my @newval=@val; shift @newval; print ">$id [ gene=$val[0] ] [ protein=@newval ]...
2503 days ago
Plot the density of genes in R
...mosome name and column2 = start position of the gene # check if ggplot2 is inst...ibrary(ggplot2) } # import a text file with gene positions # columns should b...: chr, position (no end or gene name required) genes...2274 days ago
Plot custom gene density with R
library(karyoploteR) pp2240 days ago
Perl script to convert GFF 2 FASTA !
...-file => ">$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...2129 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....1501 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...1392 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...1356 days ago
