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

@article{citeulike:3014980, 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 (Go) of the native mRNA sequence against a distribution of Go 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.}, author = {Belew, Ashton and Hepler, Nicholaus and Jacobs, Jonathan and Dinman, Jonathan}, citeulike-article-id = {3014980}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-9-339}, doi = {10.1186/1471-2164-9-339}, journal = {BMC Genomics}, keywords = {bioinformatics, biology, cerevisiae, computational, database, decay, frameshift, genome, mrna, nmd, pseudoknot, rna, saccharomyces, structure, translation, virus, yeast}, number = {1}, posted-at = {2008-07-17 17:12:43}, priority = {0}, title = {PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals}, url = {http://dx.doi.org/10.1186/1471-2164-9-339}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:3014980 L3 - citeulike-article-id:3014980 N2 - 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 (Go) of the native mRNA sequence against a distribution of Go 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. IS - 1 JF - BMC Genomics TI - PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals VL - 9 KW - bioinformatics KW - biology KW - cerevisiae KW - computational KW - database KW - decay KW - frameshift KW - genome KW - mrna KW - nmd KW - pseudoknot KW - rna KW - saccharomyces KW - structure KW - translation KW - virus KW - yeast AU - Belew, Ashton AU - Hepler, Nicholaus AU - Jacobs, Jonathan AU - Dinman, Jonathan PY - 2008/// UR - http://dx.doi.org/10.1186/1471-2164-9-339 ER -