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Bioinformatics Advance Access originally published online on February 22, 2005
Bioinformatics 2005 21(10):2525-2527; doi:10.1093/bioinformatics/bti333
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

AutoMotif server: prediction of single residue post-translational modifications in proteins

Dariusz Plewczynski 1,2,*, Adrian Tkacz 1, Lucjan Stanislaw Wyrwicz 3 and Leszek Rychlewski 1

1BioInfoBank Institute, Limanowskiego 24A/16 60-744 Poznan, Poland
2Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw Warsaw, Poland
3Bioinformatics Unit, Department of Physics, Adam Mickiewicz University Poznan, Poland

*To whom correspondence should be addressed.

Summary: The AutoMotif Server allows for identification of post-translational modification (PTM) sites in proteins based only on local sequence information. The local sequence preferences of short segments around PTM residues are described here as linear functional motifs (LFMs). Sequence models for all types of PTMs are trained by support vector machine on short-sequence fragments of proteins in the current release of Swiss-Prot database (phosphorylation by various protein kinases, sulfation, acetylation, methylation, amidation, etc.). The accuracy of the identification is estimated using the standard leave-one-out procedure. The sensitivities for all types of short LFMs are in the range of 70%.

Availability: The AutoMotif Server is available free for academic use at http://automotif.bioinfo.pl/

Contact: darman{at}bioinfo.pl


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