Results for "protein%20modeling"
Bio-Scripts
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cannot open $gb_report for reading: $!"; # Flag for multiline translation;...2915 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::Escape;...2914 days ago
- #!usr/bin/perl use strict; use warnings; my %id2seq = (); my $id = 0; open F,"$ARGV[0]",or die $!; while(){ chomp; if($_ =~...
2511 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower than 2 # return a message showing the error if (scalar(@ARGV) < 2) { print "dnaloglk...2153 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 need to set the reference multifasta file name here my $...2139 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -format => '...2137 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ sudo apt install libpar-packer-perl Reading package lists... Done...1510 days ago
Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location - NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://...942 days ago
- #You typically need the corresponding genome sequence file in FASTA format. The GFF file contains information about the #features (such as genes) in the genome, including the...
93 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.gff';...93 days ago
