Identification of cyclic nucleotide gated channels using regular expressions

Handle URI:
http://hdl.handle.net/10754/562962
Title:
Identification of cyclic nucleotide gated channels using regular expressions
Authors:
Zelman, Alice K.; Dawe, Adam Sean; Berkowitz, Gerald A.
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.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Computational Bioscience Research Center (CBRC)
Publisher:
Humana Press
Journal:
Methods in Molecular Biology
Issue Date:
3-Sep-2013
DOI:
10.1007/978-1-62703-441-8-14
PubMed ID:
23681581
Type:
Article
ISSN:
10643745
ISBN:
9781627034401
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorZelman, Alice K.en
dc.contributor.authorDawe, Adam Seanen
dc.contributor.authorBerkowitz, Gerald A.en
dc.date.accessioned2015-08-03T11:17:10Zen
dc.date.available2015-08-03T11:17:10Zen
dc.date.issued2013-09-03en
dc.identifier.isbn9781627034401en
dc.identifier.issn10643745en
dc.identifier.pmid23681581en
dc.identifier.doi10.1007/978-1-62703-441-8-14en
dc.identifier.urihttp://hdl.handle.net/10754/562962en
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.en
dc.publisherHumana Pressen
dc.subjectCyclic nucleotide-binding domainen
dc.subjectCyclic nucleotide-gated channelen
dc.subjectHinge domainen
dc.subjectOrtholog identificationen
dc.subjectPHI-BLASTen
dc.subjectPhyscomitrella patensen
dc.subjectProtein motifen
dc.subjectRegular expressionsen
dc.subjectScanPrositeen
dc.titleIdentification of cyclic nucleotide gated channels using regular expressionsen
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalMethods in Molecular Biologyen
dc.contributor.institutionAgricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, Storrs, CT, United Statesen
kaust.authorDawe, Adam Seanen
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