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 language | English (US) |
|---|---|
| Title of host publication | IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM |
| DOIs | |
| State | Published - Sep 10 2008 |
| Event | IPDPS 2008 - 22nd IEEE International Parallel and Distributed Processing Symposium - Miami, FL, United States Duration: Apr 14 2008 → Apr 18 2008 |
Publication series
| Name | IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM |
|---|
Conference
| Conference | IPDPS 2008 - 22nd IEEE International Parallel and Distributed Processing Symposium |
|---|---|
| Country | United States |
| City | Miami, FL |
| Period | 4/14/08 → 4/18/08 |
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ASJC Scopus subject areas
- Hardware and Architecture
- Software
- Electrical and Electronic Engineering
Cite this
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 proceeding › Conference contribution
}
TY - GEN
T1 - A parallel architecture for regulatory motif algorithm assessment
AU - Quest, Daniel
AU - Cooper, Kathryn M
AU - Shafiullah, Mohammad
AU - Bastola, Dhundy Raj
AU - Ali, Hesham H
PY - 2008/9/10
Y1 - 2008/9/10
N2 - 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.
AB - 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.
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U2 - 10.1109/IPDPS.2008.4536178
DO - 10.1109/IPDPS.2008.4536178
M3 - Conference contribution
SN - 9781424416943
T3 - IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM
BT - IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM
ER -