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Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM

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Bioinformatics for DNA Sequence Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 537))

Abstract

Reliable detection of cis-regulatory elements in promoter regions is a difficult and unsolved problem in computational biology. The intricacy of transcriptional regulation in higher eukaryotes, primarily in metazoans, could be a major driving force of organismal complexity. Eukaryotic genome annotations have improved greatly due to large-scale characterization of full-length cDNAs, transcriptional start sites (TSSs), and comparative genomics. Regulatory elements are identified in promoter regions using a variety of enumerative or alignment-based methods. Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program.

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Acknowledgments

This research was supported by the Intramural Research Program of the NIH, NLM, NCBI.

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Authors and Affiliations

  1. Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Leonardo Mariño-Ramírez, Kannan Tharakaraman, John L. Spouge & David Landsman

Authors
  1. Leonardo Mariño-Ramírez
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  2. Kannan Tharakaraman
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  3. John L. Spouge
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  4. David Landsman
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Editor information

Editors and Affiliations

  1. Dept. Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, 36310, Spain

    David Posada

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Mariño-Ramírez, L., Tharakaraman, K., Spouge, J.L., Landsman, D. (2009). Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_13

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  • DOI: https://doi.org/10.1007/978-1-59745-251-9_13

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-910-9

  • Online ISBN: 978-1-59745-251-9

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