SW#-GPU-enabled exact alignments on genome scale

被引：42

作者：

Korpar, Matija ^{[1
]}

Sikic, Mile ^{[1
,2
]}

机构：

[1] Univ Zagreb, Fac Elect Engn & Comp, HR-10000 Zagreb, Croatia

[2] ASTAR, Bioinformat Inst, Singapore 138671, Singapore

来源：

BIOINFORMATICS | 2013年 / 29卷 / 19期

关键词：

LINEAR-SPACE; SUBSEQUENCES; SEQUENCE; SEARCH;

D O I：

10.1093/bioinformatics/btt410

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We propose SW#, a new CUDA graphical processor unit-enabled and memory-efficient implementation of dynamic programming algorithm, for local alignment. It can be used as either a stand-alone application or a library. Although there are other graphical processor unit implementations of the Smith-Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.

引用

页码：2494 / 2495

页数：2

共 10 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2]

Flicek P, 2009, NAT METHODS, V6, pS6, DOI [10.1038/NMETH.1376, 10.1038/nmeth.1376]

[3] LINEAR SPACE ALGORITHM FOR COMPUTING MAXIMAL COMMON SUBSEQUENCES [J].

HIRSCHBERG, DS .

COMMUNICATIONS OF THE ACM, 1975, 18 (06) :341-343

[4] Versatile and open software for comparing large genomes [J].

Kurtz, S ;

Phillippy, A ;

Delcher, AL ;

Smoot, M ;

Shumway, M ;

Antonescu, C ;

Salzberg, SL .

GENOME BIOLOGY, 2004, 5 (02)

[5] OPTIMAL ALIGNMENTS IN LINEAR-SPACE [J].

MYERS, EW ;

MILLER, W .

COMPUTER APPLICATIONS IN THE BIOSCIENCES, 1988, 4 (01) :11-17

[6] A GENERAL METHOD APPLICABLE TO SEARCH FOR SIMILARITIES IN AMINO ACID SEQUENCE OF 2 PROTEINS [J].

NEEDLEMAN, SB ;

WUNSCH, CD .

JOURNAL OF MOLECULAR BIOLOGY, 1970, 48 (03) :443-+

[7] Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU [J].

Sandes, Edans Flavius de O. ;

de Melo, Alba Cristina M. A. .

IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 2013, 24 (05) :1009-1021

[8] Human-mouse alignments with BLASTZ [J].

Schwartz, S ;

Kent, WJ ;

Smit, A ;

Zhang, Z ;

Baertsch, R ;

Hardison, RC ;

Haussler, D ;

Miller, W .

GENOME RESEARCH, 2003, 13 (01) :103-107

[9] IDENTIFICATION OF COMMON MOLECULAR SUBSEQUENCES [J].

SMITH, TF ;

WATERMAN, MS .

JOURNAL OF MOLECULAR BIOLOGY, 1981, 147 (01) :195-197

[10] ALGORITHMS FOR APPROXIMATE STRING MATCHING [J].

UKKONEN, E .

INFORMATION AND CONTROL, 1985, 64 (1-3) :100-118

← 1 →