Variable Of The Optimal Search-based Gene Splicing Prediction

Alternative splicing is the RNA splicing variation mechanism in which the exons of the primary gene transcript, the pre-mRNA, are separated and reconnected so as to produce alternative ribonucleotide arrangements. These linear combinations then undergo the process of translation where specific and unique sequences of amino acids are specified, resulting in isoform proteins. It has great contribution in protein diversities and regularization of life progress. Therefore, the researches of alternative splicing are very important in studying genes regularization and protein synthesis.After analyzed both the advantages and disadvantages of traditional algorithms and software for detecting alternative splicing events, a new plan is proposed for searching patterns of alternative splicing. The algorithm of the plan is found on a hypothesis: the best alignment results are the same between cDNA vs corresponding genes and cDNA vs mRNA. With this algorithm, a platform for predicting patterns of alternative splicing which based on optimal search is built. Furthermore, an alternative splicing database is created with the help of this algorithm, and final results can be viewed on a website. Here are the works that have done:First of all, the theory basis and the reason for doing alternative splicing research are introduced and current progress and methods for searching alternative splicing are systematically summarized.Secondly, modules for certain purpose, including data downloading, validation, preprocessing and database interface are designed and developed.Thirdly, the module which based on BLAST for searching alternative splicing and correlated Parser module are designed and developed.The fourth, an alternative splicing database for rice is created.The fifth, Gbrowse is used as result view for alternative splicing information.At last, a web-based operation platform for back-end control and management is designed and created. Through these work, the platform can be used for predicting alternative splicing patterns of rice, which may guide the related experiments in labs.