Persistent Link:
http://hdl.handle.net/10150/610143
Title:
A survey of DNA motif finding algorithms
Author:
Das, Modan; Dai, Ho-Kwok
Affiliation:
Computer Science Department, Oklahoma State University, Stillwater, Oklahoma 74078, USA; USDA-ARS, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Issue Date:
2007
Publisher:
BioMed Central
Citation:
BMC Bioinformatics 2007, 8(Suppl 7):S21 doi:10.1186/1471-2105-8-S7-S21
Journal:
BMC Bioinformatics
Rights:
© 2007 Das and Dai; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especially the binding sites in deoxyribonucleic acid (DNA) for transcription factors. These binding sites are short DNA segments that are called motifs. Recent advances in genome sequence availability and in high-throughput gene expression analysis technologies have allowed for the development of computational methods for motif finding. As a result, a large number of motif finding algorithms have been implemented and applied to various motif models over the past decade. This survey reviews the latest developments in DNA motif finding algorithms.RESULTS:Earlier algorithms use promoter sequences of coregulated genes from single genome and search for statistically overrepresented motifs. Recent algorithms are designed to use phylogenetic footprinting or orthologous sequences and also an integrated approach where promoter sequences of coregulated genes and phylogenetic footprinting are used. All the algorithms studied have been reported to correctly detect the motifs that have been previously detected by laboratory experimental approaches, and some algorithms were able to find novel motifs. However, most of these motif finding algorithms have been shown to work successfully in yeast and other lower organisms, but perform significantly worse in higher organisms.CONCLUSION:Despite considerable efforts to date, DNA motif finding remains a complex challenge for biologists and computer scientists. Researchers have taken many different approaches in developing motif discovery tools and the progress made in this area of research is very encouraging. Performance comparison of different motif finding tools and identification of the best tools have proven to be a difficult task because tools are designed based on algorithms and motif models that are diverse and complex and our incomplete understanding of the biology of regulatory mechanism does not always provide adequate evaluation of underlying algorithms over motif models.
EISSN:
1471-2105
DOI:
10.1186/1471-2105-8-S7-S21
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2105/8/S7/S21

Full metadata record

DC FieldValue Language
dc.contributor.authorDas, Modanen
dc.contributor.authorDai, Ho-Kwoken
dc.date.accessioned2016-05-20T08:59:30Z-
dc.date.available2016-05-20T08:59:30Z-
dc.date.issued2007en
dc.identifier.citationBMC Bioinformatics 2007, 8(Suppl 7):S21 doi:10.1186/1471-2105-8-S7-S21en
dc.identifier.doi10.1186/1471-2105-8-S7-S21en
dc.identifier.urihttp://hdl.handle.net/10150/610143-
dc.description.abstractBACKGROUND:Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especially the binding sites in deoxyribonucleic acid (DNA) for transcription factors. These binding sites are short DNA segments that are called motifs. Recent advances in genome sequence availability and in high-throughput gene expression analysis technologies have allowed for the development of computational methods for motif finding. As a result, a large number of motif finding algorithms have been implemented and applied to various motif models over the past decade. This survey reviews the latest developments in DNA motif finding algorithms.RESULTS:Earlier algorithms use promoter sequences of coregulated genes from single genome and search for statistically overrepresented motifs. Recent algorithms are designed to use phylogenetic footprinting or orthologous sequences and also an integrated approach where promoter sequences of coregulated genes and phylogenetic footprinting are used. All the algorithms studied have been reported to correctly detect the motifs that have been previously detected by laboratory experimental approaches, and some algorithms were able to find novel motifs. However, most of these motif finding algorithms have been shown to work successfully in yeast and other lower organisms, but perform significantly worse in higher organisms.CONCLUSION:Despite considerable efforts to date, DNA motif finding remains a complex challenge for biologists and computer scientists. Researchers have taken many different approaches in developing motif discovery tools and the progress made in this area of research is very encouraging. Performance comparison of different motif finding tools and identification of the best tools have proven to be a difficult task because tools are designed based on algorithms and motif models that are diverse and complex and our incomplete understanding of the biology of regulatory mechanism does not always provide adequate evaluation of underlying algorithms over motif models.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/8/S7/S21en
dc.rights© 2007 Das and Dai; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleA survey of DNA motif finding algorithmsen
dc.typeArticleen
dc.identifier.eissn1471-2105en
dc.contributor.departmentComputer Science Department, Oklahoma State University, Stillwater, Oklahoma 74078, USAen
dc.contributor.departmentUSDA-ARS, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USAen
dc.identifier.journalBMC Bioinformaticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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