Research And Construction Of Cotton Bioinformatics Analysis System Based On Go

As the Human Genome Project and various model organism genome projects have been completed, the research focus in bioinformatics is no longer the accumulation of biological data but rather the integration processing of biological data, the construction of bioinformatics analysis system with the basis to integrate heterogeneous biological data has become a hot field in bioinformatics.In recent years, cotton genome research produced vast amounts of biological data. In order to store and analyse the data, special databases for cotton such as CMD, CottonDB, and Tropgene DB and so on have been established gradually abroad. However, analytical services provided by these databases are usually simple, for example, they just provide BLAST and CMap service and can not be extended in function, so they can not meet the needs for individual research. More importantly, the data in these databases are usually cotton-related, they do not make effective methods to integrate other heterogeneous databases (such as GenBank and SWISS-PROT, etc.) organically in biological semantic level, so they can not carry out the comparative analysis among species. In China, the cotton research institutions represented by Nanjing Agricultural University, their research such as genetic maps and other data have been included by some foreign database, but the institutions themselves do not have a complete cotton bioinformatics database and its application analysis system. Therefore, the construction of cotton bioinformatics analysis system with semantic unification and powerful analysis function, used to guide molecular design of cotton breeding, is significant.This paper does the following research:First, do the summary research in fields from the connotation of bioinformatics analysis system to the cotton bioinformatics database at home and abroad,then point out the shortcomings of existing research, introduce the concept and method of GO(Gene Ontology) and propose a vision to build the cotton bioinformatics analysis system based on GO. Second, research the internal structure of GO and its applications in bioinformatics as an important aspect after studying the basic concept of ontology. Then, research the methods to measure semantic similarity between two GO terms and point out that the semantic similarity measure between two GO terms is an important approach to solve the problem of semantic heterogeneous in biological data.Third, analyse the necessity to develop the sequence analysis software, and refer the organizational structure of the existing bioinformatics software packages, then design and develop the sequence analysis software package according to actual needs of cotton bioinformatics analysis by perl language.The package covers the sequence acquirement and selection program, EST-SSR molecular marker development program, homology analysis program, functional annotation program, and so on. This paper only develops partial software in the package.Fourth, design and implement the cotton bioinformatics analysis system based on GO semantic model under B/S structure.The system unified external databases in biological semantic level by the correspondence between GO terms and the entries annotated by GO. On this basis, the system provides more complete service such as GO-based functional annotation, similarity search, and document retrieval and so on.In this paper, GO and relational databases are used together to do cross-species comparison and analysis among genes which affected the cotton growth and development, production, quality, resistance and so on, this method is a comparative novel way of thinking. The design and implementation of GO-based cotton bioinformatics analysis system is the first attempt in the domestic cotton bioinformatics database construction, and it is positive and significant for the molecular design of cotton breeding.