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    Identification of cyclic nucleotide gated channels using regular expressions

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    Type
    Article
    Authors
    Zelman, Alice K.
    Dawe, Adam Sean
    Berkowitz, Gerald A.
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Office of the VP
    Date
    2013-09-03
    Permanent link to this record
    http://hdl.handle.net/10754/562962
    
    Metadata
    Show full item record
    Abstract
    Cyclic nucleotide-gated channels (CNGCs) are nonselective cation channels found in plants, animals, and some bacteria. They have a six-transmembrane/one- pore structure, a cytosolic cyclic nucleotide-binding domain, and a cytosolic calmodulin-binding domain. Despite their functional similarities, the plant CNGC family members appear to have different conserved amino acid motifs within corresponding functional domains than animal and bacterial CNGCs do. Here we describe the development and application of methods employing plant CNGC-specific sequence motifs as diagnostic tools to identify novel candidate channels in different plants. These methods are used to evaluate the validity of annotations of putative orthologs of CNGCs from plant genomes. The methods detail how to employ regular expressions of conserved amino acids in functional domains of annotated CNGCs and together with Web tools such as PHI-BLAST and ScanProsite to identify novel candidate CNGCs in species including Physcomitrella patens. © Springer Science+Business Media New York 2013.
    Publisher
    Humana Press
    Journal
    Methods in Molecular Biology
    ISBN
    9781627034401
    DOI
    10.1007/978-1-62703-441-8-14
    10.1007/978-1-62703-441-8_14
    PubMed ID
    23681581
    ae974a485f413a2113503eed53cd6c53
    10.1007/978-1-62703-441-8-14
    Scopus Count
    Collections
    Articles; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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