Design And Build A Platform Of Comparative Genomics

In recent years, along with the rapid development of high-speed sequencing technologies and the implementation of many whole genome sequencing project, genome data will rapid growth. The function analysis of Large genome-wide data needs new algorithm, software, and the strong support of the computing platform. This paper introduces the comparative genomics, comparative genomics analysis method, application and future development, point out the existing problem of comparative genomics, for example every software have their special data input and output format. Different software use different algorithms and emphasis, Some only can be used in certain operating system. in addition, the same sequence use different parameters will lead to different results. All of that results in some problems in the analysis of comparative genomics. And it also noted that a whole genome data are very large, especially for multiple genome alignment, requires a lot of time and storage space, the personal computer often cannot meet the requirements.In view of the above problems we developed a comparative genomics analysis platform for biological users. The platform using Browser/Server network structure, user can submit her data and parameter to platform server through the web Browser, then the server analysis the submitted data。After the analysis, results will return to user by Browser or email. The platform server are a PowerCluster8000IN computer with Linux operating system, network server use Apache HTTP, data management by using MySQL, using Perl program language for system development, HTML is used to design websites. the platform can accept the file of fasta, multi-fasta, genebank formats and also accept user submitted sequence as input data, the results output in the form of table, text or graphics.The main functions of platform are:1. Genome comparison:looking for genomic with linear area between the genome, genome reorganization (indel, repeat, rearrange and horizontal gene transfer), SNPs and copy number variation.2.Genome analysis:genome sequence composition analysis, gene prediction, rRNA and tRNA gene identification and repeat sequences search.3. Genome alignment visualization:a dynamic interface that can genome alignment results of synteny segment, insert and delete regions.Finally, in the platform, Through analysis the homology of 10 new strains of influenza A virus, indicated that PB1 gene might evolve from human H3N2 viruses, PB2,PA gene might evolve from avian H3N2 viruses and HA,NS gene might evolve from swine H1N1 viruses. Through alignment 33 genome of Mycobacterium tuberculosis and related stains, found that sequences insertion/deletion and duplication are the major source of genomic differences.