ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability
1 Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan, 2 Department of Developmental Biology and Neuroscience, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan, 3 Science of Bioresources Program, The United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan and 4 Department of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
* To whom correspondence should be addressed. Tel: +81 172 39 3638; Fax: +81 172 39 3638; Email: slsimi{at}si.hirosaki-u.ac.jp
Received February 7, 2004; Revised and Accepted March 15, 2004
ConPred II (http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/) is a server for the prediction of transmembrane (TM) topology [i.e. the number of TM segments (TMSs), TMS positions and N-tail location] based on a consensus approach by combining the results of several proposed methods. The ConPred II system is constructed from ConPred_elite and ConPred_all (previously named ConPred), proposed earlier by our group. The prediction accuracy of ConPred_elite is almost 100%, which is achieved by sacrificing the prediction coverage (20–30%). ConPred_all predicts TM topologies for all the input sequences with accuracies improved by up to 11% over individual proposed methods. In the ConPred II system, the TM topology prediction of input TM protein sequences is executed following a two-step process: (i) input sequences are first run through the ConPred_elite program; (ii) sequences for which ConPred_elite does not give the TM topology are delivered to the ConPred_all program for TM topology prediction. Users can get access to the ConPred II system automatically by submitting sequences to the server. The ConPred II server will return the predicted TM topology models and graphical representations of their contents (hydropathy plots, helical wheel diagrams of predicted TMSs and snake-like diagrams).
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