BMC Genomics Database PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals Ashton T Belew1, Nicholas L Hepler1, Jonathan L Jacobs1,2 and Jonathan D Dinman*1 BioMed Central Open Access Address: 1Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20854, USA and 2Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Building 6A/3A03, Bethesda, MD 20892, USA Email: Ashton T Belew - abelew@umd.edu; Nicholas L Hepler - nlhepler@umd.edu; Jonathan L Jacobs - jacobsjon@mail.nih.gov; Jonathan D Dinman* - dinman@umd.edu * Corresponding author Published: 17 July 2008 BMC Genomics 2008, 9:339 doi:10.1186/1471-2164-9-339 This article is available from: http://www.biomedcentral.com/1471-2164/9/339 Received: 24 January 2008 Accepted: 17 July 2008 © 2008 Belew et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract 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 (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. Conclusion: 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. Background Canonical decoding of the genetic code requires translat- ing ribosomes to convert triplets of bases (codons) into amino acid sequences. Although this is algorithm is employed for translation of the vast majority of mRNA sequences, in some special cases cis-acting mRNA ele- ments direct ribosomes into alternative reading frames, dynamically "recoding" their sequence information (reviewed in [1]). Programmed -1 Ribosomal Frameshift- ing (-1 PRF) was first discovered in RNA viruses where it enables viral genomes to encode multiple peptides from a single mRNA [2]. An individual -1 PRF signal consists of a heptameric 'slippery site' usually followed by an mRNA pseudoknot secondary structure separated by a suitable spacer region (reviewed in [3-5]). Unlike their viral coun- terparts, eukaryotic genome-encoded -1 PRF signals are predicted to direct elongating ribosomes into premature termination codons (reviewed in [6]). Such events have been shown to initiate rapid mRNA degradation in yeast through the Nonsense Mediated Decay (NMD) pathway Page 1 of 7 (page number not for citation purposes)