GBKParser, a simple tool for parsing basic gene information from a genbank file.

Typically, a genome-scale metabolic network reconstruction is begun with its genome annotation. A biochemical-reaction network is reconstructed based on the functions of gene products. Therefore, genomic information deposited in GenBank or RefSeq can be effectively used to reconstruct a metabolic network.

GBKParser will parse the useful features, e.g. Locus Tag, Gene name, Coordination, Product and EC Number, from the genbank file. Besides, GBKParser will also generate a FASTA file containing the amino acids sequences and Locus Tag in the header line.

Therefore, with the aid of GBKParser, users can start to reconstruct a genome-scale metabolic network in the GEMSiRV.

An example:

You can download the genome file (NC_000913.gbk) for Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome, then get NC 000913.gbk.xls by using GBKPaser.

Demo GBKParser.png

You should have Java Runtime Environment (JRE) before you run GBKParser.

Download GBKParser