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Bioinformatics. 2015 Nov 1;31(21):3483-91. doi: 10.1093/bioinformatics/btv403. Epub 2015 Jul 2.

JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs.

Author information

1
CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis.
2
CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and.
3
Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de bioinformatique, Conservatoire national des arts et métiers (Cnam), Paris, France.

Abstract

MOTIVATION:

Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs.

RESULTS:

JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files.

AVAILABILITY AND IMPLEMENTATION:

JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported.

CONTACT:

guillaume.beauclair@inserm.fr

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26142185
DOI:
10.1093/bioinformatics/btv403
[Indexed for MEDLINE]

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