Survey on index based homology search algorithms

被引：6

作者：

Jiang, Xianyang

Zhang, Peiheng

Liu, Xinchun

Yau, Stephen S-T.

机构：

[1] Inst Natl Rech Informat & Automat, IRISA, F-35042 Rennes, France

[2] Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China

[3] Univ Illinois, MSCS, Chicago, IL 60607 USA

[4] E China Normal Univ, Inst Math, Shanghai 200062, Peoples R China

来源：

JOURNAL OF SUPERCOMPUTING | 2007年 / 40卷 / 02期

基金：

中国国家自然科学基金;

关键词：

algorithm; bioinformatics; genomic indexing; homology search; sequence alignment; SEQUENCE; RETRIEVAL;

D O I：

10.1007/s11227-006-0041-0

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Up to now, there are many homology search algorithms that have been investigated and studied. However, a good classification method and a comprehensive comparison for these algorithms are absent. This is especially true for index based homology search algorithms. The paper briefly introduces main index construction methods. According to index construction methods, index based homology search algorithms are classified into three categories, i.e., length based index ones, transformation based index ones, and their combination. Based on the classification, the characteristics of the currently popular index based homology search algorithms are compared and analyzed. At the same time, several promising and new index techniques are also discussed. As a whole, the paper provides a survey on index based homology search algorithms.

引用

页码：185 / 212

页数：28

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