Comparing approaches to predict transmembrane domains in protein sequences

Authors:
Paul Davidsson;Johan Hagelbäck;Kenny Svensson
Affiliations:
Blekinge Institute of Technology, Ronneby, Sweden;Travelstart Nordic, Helsingborg, Sweden;Ericsson AB, Karlskrona, Sweden
Venue:
Proceedings of the 2005 ACM symposium on Applied computing
Year:
2005

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Abstract

There are today several systems for predicting transmembrane domains in membrane protein sequences. As they are based on different classifiers as well as different pre- and post-processing techniques, it is very difficult to evaluate the performance of the particular classifier used. We have developed a system called MemMiC for predicting transmembrane domains in protein sequences with the possibility to choose between different approaches to pre- and post-processing as well as different classifiers. Therefore it is possible to compare the performance of each classifier in a certain environment as well as the different approaches to pre- and post-processing. We have demonstrated the usefulness of MemMiC in a set of experiments, which shows, e.g., that the performance of a classifier is very dependent on which pre- and post-processing techniques are used.