AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses

Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We...

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Detalles Bibliográficos
Autores principales: Shi, Jiantao, Yang, Wentao, Chen, Mingjie, Du, Yanzhi, Zhang, Ji, Wang, Kankan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171486/
https://www.ncbi.nlm.nih.gov/pubmed/21931761
http://dx.doi.org/10.1371/journal.pone.0024576
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author Shi, Jiantao
Yang, Wentao
Chen, Mingjie
Du, Yanzhi
Zhang, Ji
Wang, Kankan
author_facet Shi, Jiantao
Yang, Wentao
Chen, Mingjie
Du, Yanzhi
Zhang, Ji
Wang, Kankan
author_sort Shi, Jiantao
collection PubMed
description Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous.
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spelling pubmed-31714862011-09-19 AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses Shi, Jiantao Yang, Wentao Chen, Mingjie Du, Yanzhi Zhang, Ji Wang, Kankan PLoS One Research Article Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous. Public Library of Science 2011-09-12 /pmc/articles/PMC3171486/ /pubmed/21931761 http://dx.doi.org/10.1371/journal.pone.0024576 Text en Shi et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Shi, Jiantao
Yang, Wentao
Chen, Mingjie
Du, Yanzhi
Zhang, Ji
Wang, Kankan
AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
title AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
title_full AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
title_fullStr AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
title_full_unstemmed AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
title_short AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
title_sort amd, an automated motif discovery tool using stepwise refinement of gapped consensuses
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171486/
https://www.ncbi.nlm.nih.gov/pubmed/21931761
http://dx.doi.org/10.1371/journal.pone.0024576
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