High Performance Alterantive Splicing Pattern Search Algorithms And Softwares Based On Sequence Alignment

Alternative Splicing is a process that one kind of pre-mRNA producing various mRNA isoforms by different splicing methods. It not only contributes to an extremely diverse eukaryote proteome that is expressed from a relatively small number of genes but it also allows regulated expression of these protein isoforms in response to a wide range of cues. Studying alternative splicing mechanism is of great significance to understanding eukaryote gene regulation.Based on the analysis of existing cDNA-genome alignment algorithms, a general framework of cDNA-genome computation is carried out. And within this framework, we introduce a strategy of designing high-performance alternative splicing pattern search algorithm: predicting alternative splicing patterns of a gene by combining the gene's known splicing information with its homological cDNA segments.Using this strategy, we develop two alternative splicing search algorithms: ASA (Alternative Splicing Assembler) algorithm based on BLAST software, and a high performance alternative splicing pattern search algorithm -- ASDT (Alternative Splicing Discover Tool).ASA computes splicing patterns by applying graph algorithms to BLAST search results. It employs a two-step strategy, which first maps cDNAs on known splicing isoforms, and then fixes the unmapped regions. Such strategy fulfills the demand of alternative splicing studies, and...