Construction And Application Of Cotton Molecular Biology Databases

According to actual cotton genetics and breeding, the cotton special molecular biologydatabases and the professional website of cotton genetics and breeding lab wereconstructed in the Linux operation system, which were based on the public databases in theInternet. The standalone of wwwBLAST service was realized in the apache environment.Using phrap and blast softwares, Nucleotide Sequences Extension System in silico (NSES)was set up. On a genomic scale, the ESTs of three cotton species (Gossypium hirsutum,Gossypium arboreum and Gossypium raimondii) were analysed and compared inhomology. The mainly results were as follows:1. The professional website of cotton genetics and breeding lab was constructed inDreamweave. The cotton molecular biology database system was constructed in theLinux operation system. In the database system, MySQL database was used as abackground, and PHP was used as an open language, and Apache was depended on asa server. The database system contained user registration system, database querysystem and database management system. The query system was composed of ESTdatabase, STS database, GSS database, primer database and Arabidopsis referencedatabase. The record of EST database was beyond 280,000.2. In the Linux operation system, based on Apache environment, the standalone ofwwwBLAST alignment system services was accomplished. The blast could beoperated in the off-line state. The style of retrieve, parameters selection and the patternof results were the same as NCBI's. The service could make up the alignment resultswhich were complicated and deficient of pertinency in public databases. The dataquery and sequence blast of the cotton became quicker, stabler, safer and moreconvenient.3. In Linux operation system, using phrap and blast software, Nucleotide SequencesExtension System in silico (NSES) were established in perl and shell language. TheESTs of cotton could be extended effectively and promptly in the cotton databases.The extended results could be validated by RACE, as important references to get thewhole cDNA sequences of new genes.4. On a genomic scale, the ESTs of three cotton species (G. hirsutum, G. arboreum andG. raimondii) were analysed and compared, by the BLAST and GO in homology. Theresult showed a high conservation in the GC content, function and homology analysis. The ESTs of three cotton species were searched against the rice protein database,Arabidopsis database and the EST assemblies of other plants, by BLASTX, BLASTN,TBLASTX. The unique sequences of each species were as follows: 3134 ESTs in G.hirsutum, 1577 ESTs in G. arboreum and 2508 ESTs in G. raimondii.