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dc.contributor.authorKazan, Hilal
dc.contributor.authorMorris, Quaid
dc.date.accessioned2019-12-20T08:15:25Z
dc.date.available2019-12-20T08:15:25Z
dc.date.issued2013
dc.identifier.citationKazan, H., & Morris, Q. (2013). RBPmotif a web server for the discovery of sequence and structure preferences of RNA binding proteins. Nucleic Acids Research, 41(W1), 180–186.en_US
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/20.500.12566/169
dc.description.abstractRBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif provides two types of analysis: (i) de novo motif finding when there is no a priori knowledge on RBP’s binding preferences and (ii) analysis of structure preferences when there is a previously identified sequence motif for the RBP. De novo motif finding is performed with the previously published RNAcontext algorithm that learns discriminative motif models to identify both sequence and structure preferences. The results of this analysis include the inferred binding preferences of the RBP and the added predictive value of incorporating structure preferences. Second type of analysis investigates whether the instances of the previously identified sequence motif are enriched in a particular structure context in bound sequences, relative to its instances in unbound sequences. On completion, the results page shows the comparison of structure contexts of the motif instances between bound and unbound sequences and an assessment of statistical significance of detected preferences. In summary, RBPmotif web server enables the concurrent analysis of sequence and structure preferences of RBPs through a user-friendly interface.en_US
dc.description.sponsorshipNo sponsoren_US
dc.language.isoengen_US
dc.publisherNucleic acids researchen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectSecondary structureen_US
dc.subjectİkincil yapıtr_TR
dc.subjectMotifsen_US
dc.subjectMotiflertr_TR
dc.subjectIdentificationen_US
dc.subjectKimliktr_TR
dc.subjectRecognitionen_US
dc.subjectTanımaen_US
dc.subjectAlgorithmen_US
dc.subjectAlgoritmatr_TR
dc.subjectSitesen_US
dc.subjectSitelertr_TR
dc.subjectClipen_US
dc.subjectKlipstr_TR
dc.titleRBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteinsen_US
dc.typeinfo:eu-repo/semantics/articleen_US
dc.relation.publicationcategoryInternational publicationen_US
dc.identifier.wosWOS:000323603200029
dc.identifier.scopus2-s2.0-84883592184
dc.identifier.volume41
dc.identifier.issueW1
dc.identifier.startpageW180
eperson.identifier.endpageW186
dc.contributor.orcid0000-0003-2461-4579 [Kazan, Hilal]
dc.contributor.abuauthorKazan, Hilal
dc.contributor.yokid107780 [Kazan, Hilal]
dc.contributor.ScopusAuthorID35094213400 [Kazan, Hilal]
dc.identifier.PubMedID23754853
dc.identifier.doihttps://doi.org/10.1093/nar/gkt463


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