PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.

@article{citeulike:2486408, abstract = {The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating metazoan genomes (http://www.biosapiens.info). In this context, the PONGO DAS server (http://pongo.biocomp.unibo.it) provides the annotation on predictive basis for the all-alpha membrane proteins in the human genome, not only through DAS queries, but also directly using a simple web interface. In order to produce a more comprehensive analysis of the sequence at hand, this annotation is carried out with four selected and high scoring predictors: TMHMM2.0, MEMSAT, PRODIV and ENSEMBLE1.0. The stored and pre-computed predictions for the human proteins can be searched and displayed in a graphical view. However the web service allows the prediction of the topology of any kind of putative membrane proteins, regardless of the organism and more importantly with the same sequence profile for a given sequence when required. Here we present a new web server that incorporates the state-of-the-art topology predictors in a single framework, so that putative users can interactively compare and evaluate four predictions simultaneously for a given sequence. Together with the predicted topology, the server also displays a signal peptide prediction determined with SPEP. The PONGO web server is available at http://pongo.biocomp.unibo.it/pongo.}, address = {BioDec Srl, via Calzavecchio, 20/2, I-40033 Casalecchio di Reno, (BO), Italy.}, author = {Amico, M. and Finelli, M. and Rossi, I. and Zauli, A. and Elofsson, A. and Viklund, H. and von Heijne, G. and Jones, D. and Krogh, A. and Fariselli, P. and Luigi Martelli, P. and Casadio, R. }, citeulike-article-id = {2486408}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {bioinformatics, repository, transmembrane}, month = {July}, number = {Web Server issue}, posted-at = {2008-03-07 18:08:42}, priority = {2}, title = {PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16844984}, volume = {34}, year = {2006} }

TY - JOUR ID - citeulike:2486408 L3 - citeulike-article-id:2486408 TI - PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. JF - Nucleic Acids Res VL - 34 IS - Web Server issue AD - BioDec Srl, via Calzavecchio, 20/2, I-40033 Casalecchio di Reno, (BO), Italy. SN - 1362-4962 N2 - The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating metazoan genomes (http://www.biosapiens.info). In this context, the PONGO DAS server (http://pongo.biocomp.unibo.it) provides the annotation on predictive basis for the all-alpha membrane proteins in the human genome, not only through DAS queries, but also directly using a simple web interface. In order to produce a more comprehensive analysis of the sequence at hand, this annotation is carried out with four selected and high scoring predictors: TMHMM2.0, MEMSAT, PRODIV and ENSEMBLE1.0. The stored and pre-computed predictions for the human proteins can be searched and displayed in a graphical view. However the web service allows the prediction of the topology of any kind of putative membrane proteins, regardless of the organism and more importantly with the same sequence profile for a given sequence when required. Here we present a new web server that incorporates the state-of-the-art topology predictors in a single framework, so that putative users can interactively compare and evaluate four predictions simultaneously for a given sequence. Together with the predicted topology, the server also displays a signal peptide prediction determined with SPEP. The PONGO web server is available at http://pongo.biocomp.unibo.it/pongo. KW - bioinformatics KW - repository KW - transmembrane AU - Amico, M AU - Finelli, M AU - Rossi, I AU - Zauli, A AU - Elofsson, A AU - Viklund, H AU - von Heijne, G AU - Jones, D AU - Krogh, A AU - Fariselli, P AU - Luigi Martelli, P AU - Casadio, R PY - 2006/07/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16844984 ER -