Parallel creation of non-redundant gene indices from partial mRNA transcripts

被引：14

作者：

Trivedi, N

Bischof, J

Davis, S

Pedretti, K

Scheetz, TE

Braun, TA

Roberts, CA

Robinson, NL

Sheffield, VC

Soares, AB

Casavant, TL ^{[1
]}

机构：

[1] Univ Iowa, Dept Elect & Comp Engn, Parallel Proc Lab, Iowa City, IA 52242 USA

[2] Univ Iowa, Dept Elect & Comp Engn, Coordinated Lab Computat Genom, Iowa City, IA 52242 USA

来源：

FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE | 2002年 / 18卷 / 06期

关键词：

parallel cluster application; expressed sequence tag; genome project;

D O I：

10.1016/S0167-739X(02)00059-6

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

This paper describes the UIcluster software tool, which partitions expressed sequence tag (EST) sequences and other genetic sequences into "clusters" based on sequence similarity. Ideally, each cluster will contain sequences that all represent the same gene. UIcluster has been developed over the course of 4 years to solve this problem efficiently and accurately for large data sets consisting of tens or hundreds of thousands of EST sequences. The latest version of the application has been parallelized using the MPI standard. Both the computation and memory requirements of the program can be distributed among multiple (possibly distributed) UNIX processes. (C) 2002 Elsevier Science B.V. All rights reserved.

引用

页码：863 / 870

页数：8

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