Results for "protein modeling"
Bio-Scripts
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cann...- $cds_end\n"; } elsif (/(\/translation=")(.*)/) { # protein product begins print "Translation: "; $protein...2908 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::Esc...2907 days ago
- #!usr/bin/perl use strict; use warnings; my %id2seq = (); my $id = 0; open F,"$ARGV[0]",..., $_; my @newval=@val; shift @newval; print ">$id [ gene=$val[0] ] [ protein=...
2504 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 showi...should be obtained with the two sequences: high values (positive) for coding protein...2146 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...2132 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; # Fl...ranscribed sequence (devoid of introns, but containing untranslated exons) # protein...2130 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/...P4PDB: a web tool to visualize, search and explore protein-ligand structural patternsBy...GSP4PDBwebtoolvisualizesearchexploreprotein-...1503 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slightly trouble...on construction. mcl All-vs.-all blastp + MCL clustering. mix Mixture modeling of Ks distributions. pre...1195 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 ar...gov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein...935 days ago
- #You typically need the corresponding genome sequence file in FASTA format.... #Translate the DNA sequences into protein sequences. #Simple example...om Bio.Seq import Seq def extract_protein_sequence(gff_file, genome_fas...Step 3: Translate DNA sequence into protein...
86 days ago
