Prediction of Lipoprotein and Secretory Signal Peptides in Gram-positive Bacteria with Hidden Markov Models

We present a Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins.

The method outperforms LipoP and the methods based on regular expression patterns, in various data sets containing experimentally characterized lipoproteins, secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins.

The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides.

For publication of results, please cite:
Bagos PG, Tsirigos KD, Liakopoulos TD and Hamodrakas SJ.
Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model.
J Proteome Res., 2008 Dec;7(12):5082-93

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athina University of Athens
Faculty of Biology
Dept. of Cell Biology and Biophysics
& Bioinformatics