PRFdb: a database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals.
BACKGROUND
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.


RESULTS
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 (DeltaG degrees ) of the native mRNA sequence against a distribution of DeltaG degrees values of a pool of randomized sequences derived from the original. The data have been compiled in a user-friendly, easily searchable relational database.


CONCLUSIONS
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.
Belew
Ashton T
AT
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20854, USA. abelew@umd.edu
Hepler
Nicholas L
NL
Jacobs
Jonathan L
JL
Dinman
Jonathan D
JD
D019295:Computational Biology; D003628:Database Management Systems; D018965:Frameshifting, Ribosomal; D020407:Internet; D014584:User-Computer Interface