Back to SeqWord Project main page Download Barcoding 2.0 [320 MB] Download input file example Download diagnostic barcodes Download examples of artificial metagenomes
The program BarcodeGenerator allows for the creation of barcode sequences based on a given set of genomes, it compares all pairs of genomes and select barcodes (DNA sequences) out of the core genes.
The program allows the addition of accessory genes which are genome specific to improve the sensitivity of the barcode sequences.
Another program written in Python 2.7 called the Barcoding 2.0 with a command line interface is also made available for download from the Barcoder web portal.
Barcoding 2.0 enables the practical use of metarbarcodes for visualization of distribution of the strains of interest in environmental or clinical samples.
To generate a set of barcode sequences, the user uploads the corresponding genome sequences in GenBank or FASTA format in a single archived file.
The command line tar -zcvf output_file.tar.gz input_folder is used to compress an input folder with a minimum of three genebank files
Select the gene bank file required after uploading. Maximum file size 500MB
Select the taxonomic level required (Specie, Genus, Family)
Select the required barcode length
Project name should be specified (optional)
An Email address should be entered to receive results
Upload files and barcode
The program returns a link with the generated barcode sequences in FASTA format, information on the genes selected for the barcodes and a graphical file in SVG format.
This is made up of the input folder, output folder, lib folder and run.py
The input file contains the generated barcode sequences in FASTA format
The result generated goes the output folder
The lib folder contains the built in modules which implement the set of functions for barcoding 2.0
The settings for the Python run.py includes the: I-query file, D-database name, S-stringency, R-dendogram, F-tree file, X-input folder, Z-output folder and Q-to quit
In the query file you put in the desired barcode sequences which is already in the input folder
In the database name you also put in the desired metagenome of interest which is already in the input folder
The program returns the result of the identification as a text file and in graphical SVG file. Results of identification may be better visualized, if the user provides the program with a phylogenetic tree file in text Newick or Phylip format.
The software tool Barcoder is made available at http://bargene.bi.up.ac.za/
Company Name: University of Pretoria
Website: http://bargene.bi.up.ac.za/
Email: oleg.reva@up.ac.za;
Phone number:+27-12-420-5810