Results for "miRNA target gene"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequenc...len(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-region'] == "complete":...1157 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBA...GANISM\s*)(.*)/) { print "Organism: $2\n"; } elsif(/(gene)(\s*)(\d*)(\.\.)(\d*)/) { print "Gene length: $5\n"; } elsi...2938 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...2937 days ago
- #!usr/bin/perl use strict; use warnings; my %id2seq = (); my $id...@val = split /\s+/, $_; my @newval=@val; shift @newval; print ">$id [ gene=$val[0] ] [ protein=@newval ]...
2534 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage;...->{"pid"}) && $querySeqs{$qName} && $targetSeqs{$tName}){ my %meta = (); my $shortTarget = ($tSize < $qSize) ? 1 : 0;...yed = (); foreach my $seqID (sort(keys(%targ...2329 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so...(ggplot2) } # import a text file with gene positions # columns should b...position (no end or gene name required) genes...2305 days ago
Plot custom gene density with R
library(karyoploteR) pp2270 days ago
- ➜ Tools git:(master) ✗ git clone g...x86_64-pc-linux-gnu checking target system type... x86_64-pc-linu...MP... -fopenmp checking that generated files are newer than confi...x86_64-pc-linux-gnu checking target system type... x86_64-pc-linu...MP... -fopenmp checking that generated files are newer than con...
2172 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict;...le string sub type { return 'Generic Sequence'; } # These met...nce/Nucleotide.pm use Sequence::Generic; use Sequence::Nucleotide...new Sequence::Alignment(src=>$seq,target=>$self->seq); } sub _cano...2202 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User...e = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdinetaV2.fa"; #Ur targ...2161 days ago
