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Authors: Zbigniew Szymanski 1 ; Stanisław Jankowski 2 ; Marek Dwulit 1 ; Joanna Chodzyńska 3 and Lucjan S. Wyrwicz 3

Affiliations: 1 Warsaw University of Technology, Institute of Computer Science, Poland ; 2 Warsaw University of Technology, Institute of Electronic Systems, Poland ; 3 Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Laboratory of Bioinformatics and Systems Biology, Poland

Abstract: The paper describes the Least Squares Support Vector Machine (LS-SVM) classifier of short amino acid sequences for the recognition of kinase-specific phosphorylation sites. The sequences are represented by the strings of 17 characters, each character denotes one amino acid. The data contains sequences reacting with 6 enzymes: PKA, PKB, PKC, CDK, CK2 and MAPK. To enable classification of such data by the LS-SVM classifier it is necessary to map symbolic data into real numbers domain and to perform pertinent feature selection. Presented method utilizes the AAindex (amino acid index) set up of values representing various physicochemical and biological properties of amino acids. Each symbol of the sequence is substituted by 193 values. Thereafter the feature selection procedure is applied, which uses correlation ranking formula and the Gram-Schmidt orthogonalization. The selection of 3-17 most pertinent features out of 3281 enabled successful classification by the LS-SVM.

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Paper citation in several formats:
Szymanski, Z.; Jankowski, S.; Dwulit, M.; Chodzyńska, J. and S. Wyrwicz, L. (2010). Pertinent Parameters Selection for Processing of Short Amino Acid Sequences. In Proceedings of the 10th International Workshop on Pattern Recognition in Information Systems (ICEIS 2010) - PRIS; ISBN 978-989-8425-14-0, SciTePress, pages 25-32. DOI: 10.5220/0003040600250032

@conference{pris10,
author={Zbigniew Szymanski. and Stanisław Jankowski. and Marek Dwulit. and Joanna Chodzyńska. and Lucjan {S. Wyrwicz}.},
title={Pertinent Parameters Selection for Processing of Short Amino Acid Sequences},
booktitle={Proceedings of the 10th International Workshop on Pattern Recognition in Information Systems (ICEIS 2010) - PRIS},
year={2010},
pages={25-32},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003040600250032},
isbn={978-989-8425-14-0},
}

TY - CONF

JO - Proceedings of the 10th International Workshop on Pattern Recognition in Information Systems (ICEIS 2010) - PRIS
TI - Pertinent Parameters Selection for Processing of Short Amino Acid Sequences
SN - 978-989-8425-14-0
AU - Szymanski, Z.
AU - Jankowski, S.
AU - Dwulit, M.
AU - Chodzyńska, J.
AU - S. Wyrwicz, L.
PY - 2010
SP - 25
EP - 32
DO - 10.5220/0003040600250032
PB - SciTePress

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