DIGAP - a Database of Improved Gene Annotation for Phytopathogens

BMC Genomics

Database

Shi-Cui Zhang¹  Ji-Wei Chang²  Hong-Yu Zhang³  Ling-Ling Chen³  Hong-Fang Ji⁴  Wei Wang⁴  Na Gao⁴  Lin Zhang⁴  Bei Gao⁵ 

[1] Department of Marine Biology, Ocean University of China, 266003, Qingdao, PR China;National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, PR China;National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, PR China;Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, 255049, Zibo, PR China;Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, 255049, Zibo, PR China;Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, 255049, Zibo, PR China;Department of Marine Biology, Ocean University of China, 266003, Qingdao, PR China;

关键词: Hypothetical Protein;    High Sequence Identity;    Prokaryotic Genome;    Translation Initiation Site;    Codon Adaptation Index;   

DOI  :  10.1186/1471-2164-11-54

 received in 2009-07-15, accepted in 2010-01-21,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundBacterial 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.DescriptionDIGAP 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% ~ 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.ConclusionThe 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/.

【 授权许可】

Unknown   
© Gao et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.