DIGA--a database of improved gene annotation for phytopathogens.
BACKGROUND
Bacterial plant pathogens are very harmful to their host plants, which can cause devastating agricultural losses in the world. With the development of microbial genome sequencing, many strains of phytopathogens have been sequenced. However, some misannotations exist in these phytopathogen genomes. Our objective is to improve these annotations and store them in a central database DIGAP.


METHODS
DIGAP includes the following improved information on phytopathogen genomes. (i) All the 'hypothetical proteins' were checked, and non-coding ORFs recognized by the Z curve method were removed. (ii) The translation initiation sites (TISs) of 20% approximately 25% of all the protein-coding genes have been corrected based on the NCBI RefSeq, ProTISA database and an ab initio program, GS-Finder. (iii) Potential functions of about 10% 'hypothetical proteins' have been predicted using sequence alignment tools. (iv) Two theoretical gene expression indices, the codon adaptation index (CAI) and the E(g) index, were calculated to predict the gene expression levels. (v) Potential agricultural bactericide targets and their homology-modeled 3D structures are provided in the database, which is of significance for agricultural antibiotic discovery.


CONCLUSIONS
The results in DIGAP provide useful information for understanding the pathogenetic mechanisms of phytopathogens and for finding agricultural bactericides. DIGAP is freely available at http://ibi.hzau.edu.cn/digap/.
Gao
Na
N
Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China.
Chen
Ling-Ling
LL
Ji
Hong-Fang
HF
Wang
Wei
W
Chang
Ji-Wei
JW
Gao
Bei
B
Zhang
Lin
L
Zhang
Shi-Cui
SC
Zhang
Hong-Yu
HY
D030541:Databases, Genetic; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D016366:Open Reading Frames; D010442:Peptide Chain Initiation, Translational; D010935:Plant Diseases / Q000382:microbiology*; D012045:Regulatory Sequences, Nucleic Acid; D014584:User-Computer Interface