A parallel architecture for regulatory motif algorithm assessment

Daniel Quest, Kathryn M Cooper, Mohammad Shafiullah, Dhundy Raj Bastola, Hesham H Ali

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Computational discovery of cis-regulatory motifs has become one of the more challenging problems in bioinformatics. In recent years, over 150 methods have been proposed as solutions, however, it remains difficult to characterize the advantages and disadvantages of these approaches because of the wide variability of approaches and datasets. Although biologists desire a set of parameters and a program most appropriate for cis-regulatory discovery in their domain of interest, compiling such a list is a great computational challenge. First, a discovery pipeline for 150+ methods must be automated and then each dataset of interest must used to grade the methods. Automation is challenging because these programs are intended to be used over a small set of sites and consequently have many manual steps intended to help the user in fine-tuning the program to specific problems or organisms. If a program is fine-tuned to parameters other than those used in the original paper, it is not guaranteed to have the same sensitivity and specificity. Consequently, there are few methods that rank motif discovery tools. This paper proposes a parallel framework for the automation and evaluation of cis-regulatory motif discovery tools. This evaluation platform can both run and benchmark motif discovery tools over a wide range of parameters and is the first method to consider both multiple binding locations within a regulatory region and regulatory regions of orthologous genes. Because of the large amount of tests required, we implemented this platform on a computing cluster to increase performance.

Original languageEnglish (US)
Title of host publicationIPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM
DOIs
StatePublished - Sep 10 2008
EventIPDPS 2008 - 22nd IEEE International Parallel and Distributed Processing Symposium - Miami, FL, United States
Duration: Apr 14 2008Apr 18 2008

Publication series

NameIPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM

Conference

ConferenceIPDPS 2008 - 22nd IEEE International Parallel and Distributed Processing Symposium
CountryUnited States
CityMiami, FL
Period4/14/084/18/08

Fingerprint

Parallel architectures
Automation
Cluster computing
Bioinformatics
Tuning
Pipelines
Genes

ASJC Scopus subject areas

  • Hardware and Architecture
  • Software
  • Electrical and Electronic Engineering

Cite this

Quest, D., Cooper, K. M., Shafiullah, M., Bastola, D. R., & Ali, H. H. (2008). A parallel architecture for regulatory motif algorithm assessment. In IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM [4536178] (IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM). https://doi.org/10.1109/IPDPS.2008.4536178

A parallel architecture for regulatory motif algorithm assessment. / Quest, Daniel; Cooper, Kathryn M; Shafiullah, Mohammad; Bastola, Dhundy Raj; Ali, Hesham H.

IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM. 2008. 4536178 (IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Quest, D, Cooper, KM, Shafiullah, M, Bastola, DR & Ali, HH 2008, A parallel architecture for regulatory motif algorithm assessment. in IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM., 4536178, IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM, IPDPS 2008 - 22nd IEEE International Parallel and Distributed Processing Symposium, Miami, FL, United States, 4/14/08. https://doi.org/10.1109/IPDPS.2008.4536178
Quest D, Cooper KM, Shafiullah M, Bastola DR, Ali HH. A parallel architecture for regulatory motif algorithm assessment. In IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM. 2008. 4536178. (IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM). https://doi.org/10.1109/IPDPS.2008.4536178
Quest, Daniel ; Cooper, Kathryn M ; Shafiullah, Mohammad ; Bastola, Dhundy Raj ; Ali, Hesham H. / A parallel architecture for regulatory motif algorithm assessment. IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM. 2008. (IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM).
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