Identification of cyclic nucleotide gated channels using regular expressions
Type
ArticleKAUST Department
Computational Bioscience Research Center (CBRC)Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Office of the VP
Date
2013-09-03Permanent link to this record
http://hdl.handle.net/10754/562962
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Show full item recordAbstract
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 PressJournal
Methods in Molecular BiologyISBN
9781627034401PubMed ID
23681581ae974a485f413a2113503eed53cd6c53
10.1007/978-1-62703-441-8-14
Scopus Count
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