FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2080286449> ?p ?o ?g. }

• W2080286449 abstract "A number of computational methods have been proposed for identifying transcription factor binding sites from a set of unaligned sequences that are thought to share the motif in question. We here introduce an algorithm, called cosmo, that allows this search to be supervised by specifying a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may be formulated, for example, on the basis of prior knowledge about the structure of the transcription factor in question. The algorithm is based on the same two-component multinomial mixture model used by MEME, with stronger reliance, however, on the likelihood principle instead of more ad-hoc criteria like the E-value. The intensity parameter in the ZOOPS and TCM models, for instance, is estimated based on a profile-likelihood approach, and the width of the unknown motif is selected based on BIC. These changes allow cosmo to outperform MEME even in the absence of any constraints, as evidenced by 2- to 3-fold greater sensitivity in some simulation studies. Additional improvements in performance can be achieved by selecting the model type (OOPS, ZOOPS, or TCM) data-adaptively or by supplying correctly specified constraints, especially if the motif appears only as a weak signal in the data. The algorithm can data-adaptively choose between working in a given constrained model or in the completely unconstrained model, guarding against the risk of supplying mis-specified constraints. Simulation studies suggest that this approach can offer 3 to 3.5 times greater sensitivity than MEME. The algorithm has been implemented in the form of a stand-alone C program as well as a web application that can be accessed at http://cosmoweb.berkeley.edu. An R package is available through Bioconductor (http://bioconductor.org)." @default.
• W2080286449 created "2016-06-24" @default.
• W2080286449 creator A5027290261 @default.
• W2080286449 creator A5055341021 @default.
• W2080286449 creator A5060422059 @default.
• W2080286449 date "2007-01-23" @default.
• W2080286449 modified "2023-09-24" @default.
• W2080286449 title "Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo" @default.
• W2080286449 cites W1214546200 @default.
• W2080286449 cites W1597226907 @default.
• W2080286449 cites W1631908837 @default.
• W2080286449 cites W1975032496 @default.
• W2080286449 cites W1984433293 @default.
• W2080286449 cites W1998300401 @default.
• W2080286449 cites W2003967338 @default.
• W2080286449 cites W2023599316 @default.
• W2080286449 cites W2027662098 @default.
• W2080286449 cites W2030703096 @default.
• W2080286449 cites W2037491422 @default.
• W2080286449 cites W2037940015 @default.
• W2080286449 cites W2041877620 @default.
• W2080286449 cites W2048869777 @default.
• W2080286449 cites W2053807426 @default.
• W2080286449 cites W2056002855 @default.
• W2080286449 cites W2058815839 @default.
• W2080286449 cites W2060161465 @default.
• W2080286449 cites W2073850887 @default.
• W2080286449 cites W2074703985 @default.
• W2080286449 cites W2082736011 @default.
• W2080286449 cites W2084620487 @default.
• W2080286449 cites W2084908610 @default.
• W2080286449 cites W2141408320 @default.
• W2080286449 cites W2144710927 @default.
• W2080286449 cites W2145295592 @default.
• W2080286449 cites W2145627818 @default.
• W2080286449 cites W2150293502 @default.
• W2080286449 cites W2150926065 @default.
• W2080286449 cites W2154447604 @default.
• W2080286449 cites W2162111678 @default.
• W2080286449 cites W2168175751 @default.
• W2080286449 cites W2319502789 @default.
• W2080286449 cites W2408204122 @default.
• W2080286449 cites W2464161892 @default.
• W2080286449 cites W2798823272 @default.
• W2080286449 doi "https://doi.org/10.2202/1544-6115.1260" @default.
• W2080286449 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/17402923" @default.
• W2080286449 hasPublicationYear "2007" @default.
• W2080286449 type Work @default.
• W2080286449 sameAs 2080286449 @default.
• W2080286449 citedByCount "37" @default.
• W2080286449 countsByYear W20802864492012 @default.
• W2080286449 countsByYear W20802864492013 @default.
• W2080286449 countsByYear W20802864492014 @default.
• W2080286449 countsByYear W20802864492015 @default.
• W2080286449 countsByYear W20802864492018 @default.
• W2080286449 countsByYear W20802864492020 @default.
• W2080286449 countsByYear W20802864492021 @default.
• W2080286449 crossrefType "journal-article" @default.
• W2080286449 hasAuthorship W2080286449A5027290261 @default.
• W2080286449 hasAuthorship W2080286449A5055341021 @default.
• W2080286449 hasAuthorship W2080286449A5060422059 @default.
• W2080286449 hasBestOaLocation W20802864492 @default.
• W2080286449 hasConcept C11413529 @default.
• W2080286449 hasConcept C119857082 @default.
• W2080286449 hasConcept C121332964 @default.
• W2080286449 hasConcept C124101348 @default.
• W2080286449 hasConcept C154945302 @default.
• W2080286449 hasConcept C24890656 @default.
• W2080286449 hasConcept C32276052 @default.
• W2080286449 hasConcept C41008148 @default.
• W2080286449 hasConceptScore W2080286449C11413529 @default.
• W2080286449 hasConceptScore W2080286449C119857082 @default.
• W2080286449 hasConceptScore W2080286449C121332964 @default.
• W2080286449 hasConceptScore W2080286449C124101348 @default.
• W2080286449 hasConceptScore W2080286449C154945302 @default.
• W2080286449 hasConceptScore W2080286449C24890656 @default.
• W2080286449 hasConceptScore W2080286449C32276052 @default.
• W2080286449 hasConceptScore W2080286449C41008148 @default.
• W2080286449 hasIssue "1" @default.
• W2080286449 hasLocation W20802864491 @default.
• W2080286449 hasLocation W20802864492 @default.
• W2080286449 hasLocation W20802864493 @default.
• W2080286449 hasOpenAccess W2080286449 @default.
• W2080286449 hasPrimaryLocation W20802864491 @default.
• W2080286449 hasRelatedWork W2961085424 @default.
• W2080286449 hasRelatedWork W3046775127 @default.
• W2080286449 hasRelatedWork W3107474891 @default.
• W2080286449 hasRelatedWork W3170094116 @default.
• W2080286449 hasRelatedWork W3209574120 @default.
• W2080286449 hasRelatedWork W4205958290 @default.
• W2080286449 hasRelatedWork W4286629047 @default.
• W2080286449 hasRelatedWork W4306321456 @default.
• W2080286449 hasRelatedWork W4306674287 @default.
• W2080286449 hasRelatedWork W4224009465 @default.
• W2080286449 hasVolume "6" @default.
• W2080286449 isParatext "false" @default.
• W2080286449 isRetracted "false" @default.
• W2080286449 magId "2080286449" @default.
• W2080286449 workType "article" @default.