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: Download the genome file (NC_000913.gbk) from ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/, then you can get NC_000913.gbk.xls by using GBKPaser.
You should have Java Runtime Environment (JRE) before you run GBKParser.
Download GBKParser