The Establishment And Application Of The Analysis Platform Of Molecular Systematics

Molecular phylogenetics is on the basis of experiment and computation. The popularity of rapid DNA sequencing technology provides large amounts of data for molecular phylogenetics, while the sequence analysis technology is the important tool to gain knowledge from data. In the genomic era, the availability of many model organisms' complete genome sequences made molecular phylogenetics facing unprecedented opportunity and challenge. On the one hand, the tree of life project is helpful to select new model organisms and launch corresponding genome projects. On the other hand, the genome projects are conductive to elucidate the evolutionary relationship among model organisms and the evolutionary mode of genome. Furthermore, the sequence analysis technology of molecular phylogenetics is becoming a powerful tool for the exploration and integration of genome data. Thus, it plays a key role in many fields of life science. Currently, phylogenomics is emerging from the intersection of molecular phylogenetics and genomics.To lay the solid foundation for information management and data analysis in molecular phylogenetics, we established the analysis platform of molecular systematics, which incorporates professional database service, data analysis technology support and related network resources.The platform includes three professional databases. The first is DNA voucher database, of which the record has seven fields, i.e., English family name, Chinese family name, Latin name, collector, collection number, area and date. Users can perform searches in the database via setting one or more fields equal to specific value. Until June 1, 2004, there were totally 3,491 records in this database. The second is primerdatabase, of which the record includes three fields, i.e., primer name, sequence content and annealing temperature. Users can also perform searches in this database. Until June 1, 2004, there were totally 170 primer records for the amplification of different DNA sequences from plant nuclear, chloroplast and mitochondrial genomes. The third is biocomputation database that provides the service of transfer and storage of sequence analysis dataset and result files for the reseachers.To ensure the safety and utility of professional databases, the interface and searching engine of databases, plus the registration program for system managers and users, were developed. The former allows users to perform data manipulation, such as upload, download and searching, while the latter sets the level of authority for different visitors. The system manager, who is responsible for the maintainance and management of platform, is superior to the user.The data analysis technology support, consisting of two parts, is designed to help users to master the general analysis methods used in molecular phylogenetics. In the effective way of data analysis, the users can be relaxed from complex statistic algorithms or computer program, and concentrate their focus on the biological interpretation of computation results.The first part briefly introduces those analysis methods in common use and lists relevant keys according to different questions in molecular phylogenetics. Those questions include phylogeny reconstruction, the estimation of substitution rate and divergence time, ancestral distribution inference, hypothesis testing of character evolution, and the detection of adaptive evolution on the codon level. As the significant progress in methodology, likelihood ratio tests and bayesian inference, which play an important role in the molecular phylogenet ics researches, were emphasized. The second part.contains many computer program orsoftware packages, related instant notes, and command modular files. After download and installation, users can perform data analysis by the use of modular files according to instant notes.Besides, some useful network resources relevant to molecular phylogenetics, such as bioinformatics centers, the laboratories of molecular evolution and phylogenetics, professional journals and databases, have been incorporated in the pl...