Speeding up pairwise sequence alignments: A scoring scheme reweighting based approach

被引：0

作者：

Gao, Yong ^{[1
]}

Henderson, Michael ^{[1
]}

机构：

[1] Univ British Columbia, Irving K Barber Sch Arts & Sci, Dept Comp Sci, Kelowna, BC V1V 1V7, Canada

来源：

PROCEEDINGS OF THE 7TH IEEE INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, VOLS I AND II | 2007年

关键词：

D O I：

暂无

中图分类号：

R318 [生物医学工程];

学科分类号：

0831 ;

摘要：

A general technique based on scoring scheme reweighting is proposed that can be used to speed up dynamic programming algorithms for a variety of pairwise sequence alignment problems. For the standard sequence alignment problem with an arbitrary gap penalty function, we show that a reweighted scoring scheme can be obtained by an efficient preprocessing step that computes a set of upper bounds on the score of the optimal alignment between pairs of suffixes of the sequences. A series of experiments on synthetic sequences and biological sequences indicate that our algorithm offers significant and robust speedup over the standard cubic-time dynamic programming algorithm. For sequences of length up to 2000 used in our experiments, the speedup factor ranges from 4 to more than 50. With a strong upper bound, a sub-cubic behavior in running time is also observed for all the tested situations.

引用

页码：1194 / 1198

页数：5