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

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1471-2164-9-339.pdf (2.14 MB)
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2008-07-17

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Belew, 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).

Abstract

The 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 .

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