PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals

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dc.contributor.authorBelew, Ashton T
dc.contributor.authorHepler, Nicholas L
dc.contributor.authorJacobs, Jonathan L
dc.contributor.authorDinman, Jonathan D
dc.date.accessioned2021-12-06T15:32:34Z
dc.date.available2021-12-06T15:32:34Z
dc.date.issued2008-07-17
dc.description.abstractThe Programmed Ribosomal Frameshift Database (PRFdb) provides an interface to help researchers identify potential programmed -1 ribosomal frameshift (-1 PRF) signals in eukaryotic genes or sequences of interest. To identify putative -1 PRF signals, sequences are first imported from whole genomes or datasets, e.g. the yeast genome project and mammalian gene collection. They are then filtered through multiple algorithms to identify potential -1 PRF signals as defined by a heptameric slippery site followed by an mRNA pseudoknot. The significance of each candidate -1 PRF signal is evaluated by comparing the predicted thermodynamic stability (ΔG°) of the native mRNA sequence against a distribution of ΔG° values of a pool of randomized sequences derived from the original. The data have been compiled in a user-friendly, easily searchable relational database. The PRFdB enables members of the research community to determine whether genes that they are investigating contain potential -1 PRF signals, and can be used as a metasource of information for cross referencing with other databases. It is available on the web at http://dinmanlab.umd.edu/prfdb .en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-9-339
dc.identifierhttps://doi.org/10.13016/imfr-w0ub
dc.identifier.citationBelew, A.T., Hepler, N.L., Jacobs, J.L. et al. PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals. BMC Genomics 9, 339 (2008).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28192
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCell Biology & Molecular Geneticsen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectMinimum Free Energyen_US
dc.subjectSequence Windowen_US
dc.subjectRibosomal Frameshiften_US
dc.subjectMinimum Free Energyen_US
dc.subjectMammalian Gene Collectionen_US
dc.titlePRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signalsen_US
dc.typeArticleen_US

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