Efficient Search of Position Weight Matrices with a Truncated Suffix Tree
The Position Weight Matrix (PWM) is a widely used model of choice for several kind of biological signals in both DNA and protein contexts. Recently, several algorithms have been proposed to speed up the time required by the basic operation of matching a matrix with a sequence. In this paper we present TruSTsearch, an offline algorithm based on the truncated suffix trees data structure. We provide experimental comparison between our algorithm and the best known offline algorithm PoSSuMsearch, based on enhanced suffix array, showing that, thanks to the specifically designed TruSTcoding, our solution requires less space, and allows better performances.
Position Weight Matrices Indexing Sequence analysis Algorithms models software and tools in Bioinformatics
Cinzia Pizzi Alessio Favaretto
Department of Information Engineering University of Padova Padova, Italy
国际会议
三亚
英文
93-97
2011-03-25（万方平台首次上网日期，不代表论文的发表时间）