Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1 Export

@article{tmhmm-2001, abstract = {We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. We present a detailed analysis of TMHMM's performance, and show that it correctly predicts 97–98 \% of the transmembrane helices. Additionally, TMHMM can discriminate between soluble and membrane proteins with both specificity and sensitivity better than 99 \%, although the accuracy drops when signal peptides are present. This high degree of accuracy allowed us to predict reliably integral membrane proteins in a large collection of genomes. Based on these predictions, we estimate that 20–30 \% of all genes in most genomes encode membrane proteins, which is in agreement with previous estimates. We further discovered that proteins with N in -C in topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans , where the large number of 7TM receptors increases the counts for N out -C in topologies. We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/ .}, address = {Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark. krogh@cbs.dtu.dk}, author = {Krogh, Anders and Larsson, Bj\"{o}rn and von Heijne, Gunnar and Sonnhammer, Erik L. L.}, citeulike-article-id = {408114}, citeulike-linkout-0 = {http://dx.doi.org/10.1006/jmbi.2000.4315}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0022283600943158}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/11152613}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=11152613}, citeulike-linkout-4 = {http://www.sciencedirect.com/science/article/B6WK7-457D7V9-K/2/0367078014042718f39416a2c3ddeeb3}, day = {19}, doi = {10.1006/jmbi.2000.4315}, issn = {00222836}, journal = {Journal of Molecular Biology}, keywords = {prok-seq-cg-pipeline}, month = {January}, number = {3}, pages = {567--580}, posted-at = {2009-11-03 20:16:03}, priority = {2}, title = {Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1}, url = {http://dx.doi.org/10.1006/jmbi.2000.4315}, volume = {305}, year = {2001} }

TY - JOUR ID - tmhmm-2001 L3 - citeulike-article-id:408114 N2 - We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. We present a detailed analysis of TMHMM’s performance, and show that it correctly predicts 97–98 % of the transmembrane helices. Additionally, TMHMM can discriminate between soluble and membrane proteins with both specificity and sensitivity better than 99 %, although the accuracy drops when signal peptides are present. This high degree of accuracy allowed us to predict reliably integral membrane proteins in a large collection of genomes. Based on these predictions, we estimate that 20–30 % of all genes in most genomes encode membrane proteins, which is in agreement with previous estimates. We further discovered that proteins with N in -C in topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans , where the large number of 7TM receptors increases the counts for N out -C in topologies. We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/ . IS - 3 JF - Journal of Molecular Biology SN - 00222836 AD - Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark. krogh@cbs.dtu.dk EP - 580 TI - Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1 VL - 305 SP - 567 KW - prok-seq-cg-pipeline AU - Krogh, Anders AU - Larsson, Björn AU - von Heijne, Gunnar AU - Sonnhammer, Erik PY - 2001/01/19/ UR - http://dx.doi.org/10.1006/jmbi.2000.4315 ER -