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    Methods Mol Biol. 2009;537:263-76.

    Promoter analysis: gene regulatory motif identification with A-GLAM.

    Source

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

    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.

    PMID:
    19378149
    [PubMed - indexed for MEDLINE]
    PMCID:
    PMC2702474
    Free PMC Article

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