一种快速可变剪接模式搜索算法的研究

Study of an efficient alternative splicing searching algorithm

提出了一种快速可变剪接模式搜索算法--ASDT.该算法通过计算cDNA与基因序列的联配结构来寻找基因的可变剪接模式.ASDT计算中引入已知剪接信息,并采用增强后缀数组、块联配延伸和K最大参考路径等技术和方法来提高计算速度.与国外的BLAT软件的比较结果显示,在达到相同计算精度的前提下,ASDT的搜索速度是BLAT的2到16倍.根据ASDT算法开发的工具可以在以下网址获得： http：//www.scbit.org/ASDT/.

The alternative splicing discover tool （ASDT）, a fast algorithm on alternative splicing pattern search, was developed recently. It can discover gene alternative-spliced variants by mapping cDNA sequences to genomes. In addition to the known gene splicing information, enhanced SUffLX arrays, algorithms of block alignment extension and K-longest reference path are also incorporated to improve computing performance as well. The comparison with the classical BLAT software in this field shows that the searching speed of ASDT reaches 2 - 16 times of the BLAT under the similar computing precision. The tool based on ASDT algorithm can be downloaded from http：//www, scbit, org/ASDT/.