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

作　　者：张欣[1] 赵静[2] 王庆康[1] 曹志伟[3] 

机构地区：[1]上海交通大学微纳科学技术研究院,微米/纳米加工技术国家重点实验室,薄膜与微细技术教育部重点实验室,上海200030 [2]上海交通大学生命科学技术学院,200240 [3]上海生物信息技术研究中心,上海200235

出　　处：《高技术通讯》2006年第10期1051-1055,共5页Chinese High Technology Letters

基　　金：973计划（2004CB720103）资助项目

摘　　要：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/.

关 键 词：可变剪接 联配搜索 算法 EST 

分 类 号：TP18[自动化与计算机技术—控制理论与控制工程]