Representative transcript sets for evaluating a translational initiation sites predictor

<p>Abstract</p> <p>Background</p> <p>Translational initiation site (TIS) prediction is a very important and actively studied topic in bioinformatics. In order to complete a comparative analysis, it is desirable to have several benchmark data sets which can be used to test the effectiveness of different algorithms. An ideal benchmark data set should be reliable, representative and readily available. Preferably, proteins encoded by members of the data set should also be representative of the protein population actually expressed in cellular specimens.</p> <p>Results</p> <p>In this paper, we report a general algorithm for constructing a reliable sequence collection that only includes mRNA sequences whose corresponding protein products present an average profile of the general protein population of a given organism, with respect to three major structural parameters. Four representative transcript collections, each derived from a model organism, have been obtained following the algorithm we propose. Evaluation of these data sets shows that they are reasonable representations of the spectrum of proteins obtained from cellular proteomic studies. Six state-of-the-art predictors have been used to test the usefulness of the construction algorithm that we proposed. Comparative study which reports the predictors' performance on our data set as well as three other existing benchmark collections has demonstrated the actual merits of our data sets as benchmark testing collections.</p> <p>Conclusion</p> <p>The proposed data set construction algorithm has demonstrated its property of being a general and widely applicable scheme. Our comparison with published proteomic studies has shown that the expression of our data set of transcripts generates a polypeptide population that is representative of that obtained from evaluation of biological specimens. Our data set thus represents "real world" transcripts that will allow more accurate evaluation of algorithms dedicated to identification of TISs, as well as other translational regulatory motifs within mRNA sequences. The algorithm proposed by us aims at compiling a redundancy-free data set by removing redundant copies of homologous proteins. The existence of such data sets may be useful for conducting statistical analyses of protein sequence-structure relations. At the current stage, our approach's focus is to obtain an "average" protein data set for any particular organism without posing much selection bias. However, with the three major protein structural parameters deeply integrated into the scheme, it would be a trivial task to extend the current method for obtaining a more selective protein data set, which may facilitate the study of some particular protein structure.</p

TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

<p>Abstract</p> <p>Background</p> <p>The nucleotide sequence flanking the translation initiation codon (start codon context) affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation initiation site (TIS) to produce proteins with different properties. Multi-targeting may reflect the translational variability of these other protein forms. In this paper we present a web server that performs computations to investigate the usage of alternative translation initiation sites for the synthesis of new protein variants that might have different functions.</p> <p>Results</p> <p>An efficient web-based tool entitled TISs-ST (Translation Initiation Sites and Secretory Targets) evaluates putative translation initiation sites and indicates the prediction of a signal peptide of the protein encoded from this site. The TISs-ST web server is freely available to both academic and commercial users and can be accessed at <url>http://ipe.cbmeg.unicamp.br/pub/TISs-ST</url>.</p> <p>Conclusion</p> <p>The program can be used to evaluate alternative translation initiation site consensus with user-specified sequences, based on their composition or on many position weight matrix models. TISs-ST provides analytical and visualization tools for evaluating the periodic frequency, the consensus pattern and the total information content of a sequence data set. A search option allows for the identification of signal peptides from predicted proteins using the PrediSi software.</p

Review of Outcomes from a Change in Faculty Clinic Management in a U.S. Dental School

Dental schools use a variety of clinic management models with the goals of promoting patient care, student education, and fiscal responsibility. In 2004, the University of the Pacific Arthur A. Dugoni School of Dentistry transitioned to a more generalist model with these goals in mind. The purpose of this study was to evaluate the outcomes of this clinic model change relative to the quantity of specific procedures completed by students. The quantity of procedures completed by each student from the classes of 1995 through 2009 were compiled from our electronic clinic management system and analyzed. The post-transition group (2004–09) showed a greater number of completed oral diagnosis and treatment planning and root planing procedures per student compared to the pre-transition group (1995–2003), but fewer crowns, root canals, operative procedures, and dentures. Because the higher procedure numbers were for low-cost procedures, our transition to a generalist model did not necessarily enhance clinic income but may support student learning and enhanced patient care

Perceptions of dental schools from within and outside the university

Perceptions of dental schools held by high-level administrators of their parent institutions and officials in the local community have great potential to influence the future of dental education. The intent of this investigation was to gain a preliminary knowledge of such perceptions at seven institutions in the United States and to use this information to formulate hypotheses that can provide the basis for further targeted investigations that provide evidence useful in decision making and planning processes within dental schools. Interviews with university administrators, executive directors of state dental associations, and state government officials in seven areas of the United States were conducted. The hypotheses drawn from these interviews are: 1) dental schools are generally too insular and need to interact more with their parent institutions and external community; 2) dental schools need to systematically and continually get the message of the value of their services out to the public and political constituencies; and 3) multidisciplinarity and integration with other units are important to university administrators but largely outside the concerns of those external to the university. We suggest that these hypotheses form the basis of subsequent, more targeted, follow-up investigations with the intent of formulating specific recommendations for action