Results for "protein"
Bio-Scripts
Parse a genbank file using regular expressions
...$cds_end = $4; print "CDS: $cds_start - $cds_end\n"; } elsif (/(\/translation=")(.*)/) { # protein product begins print "Translation: "; $protein = $2; $trans = 1;...2905 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::Es...2904 days ago
- ...~ /^>(.+)/){ $id++; s/\[//g; s/\]//g; my @val = split /\s+/, $_; my @newval=@val; shift @newval; print ">$id [ gene=$val[0] ] [ protein=@newval ]\n"; #$...
2501 days ago
Perl script to find coding regions in DNA sequences
...intron, respectively. Extremely different values of coding potential should be obtained with the two sequences: high values (positive) for coding protein sequences and low values (zer...2144 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...2129 days ago
Perl script to convert GFF 2 FASTA !
...starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of introns, but containing untranslated exons) # protein - cds translated (includes a...2127 days ago
Pack a perl program with their dependencies on Ubuntu !
...m Jha@neelam GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patternsBy...Neelam Jha yesterday GSP4PDBwebtoolvisualizesearchexploreprotein-ligandstructuralpatterns...1500 days ago
Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location - NCBI where all data...st/db/ # Database detail / description nr.*tar.gz | Non-redundant protein sequences from GenPept, Swiss...932 days ago
- ...TA format. #Translate the DNA sequences into protein sequences. #Simple example...ecord from Bio.Seq import Seq def extract_protein_sequence(gff_file, genome_fas...# Step 3: Translate DNA sequence into protein sequence gene_protein_se...
83 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.g...83 days ago
