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dc.contributor.authorZelman, Alice K.
dc.contributor.authorDawe, Adam Sean
dc.contributor.authorBerkowitz, Gerald A.
dc.date.accessioned2015-08-03T11:17:10Z
dc.date.available2015-08-03T11:17:10Z
dc.date.issued2013-09-03
dc.identifier.isbn9781627034401
dc.identifier.issn10643745
dc.identifier.pmid23681581
dc.identifier.doi10.1007/978-1-62703-441-8-14
dc.identifier.doi10.1007/978-1-62703-441-8_14
dc.identifier.urihttp://hdl.handle.net/10754/562962
dc.description.abstractCyclic 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.
dc.publisherHumana Press
dc.subjectCyclic nucleotide-binding domain
dc.subjectCyclic nucleotide-gated channel
dc.subjectHinge domain
dc.subjectOrtholog identification
dc.subjectPHI-BLAST
dc.subjectPhyscomitrella patens
dc.subjectProtein motif
dc.subjectRegular expressions
dc.subjectScanProsite
dc.titleIdentification of cyclic nucleotide gated channels using regular expressions
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentOffice of the VP
dc.identifier.journalMethods in Molecular Biology
dc.contributor.institutionAgricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, Storrs, CT, United States
kaust.personDawe, Adam Sean


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