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Bioinformatics Vol. 19 no. 1 2003
Pages 30-36
© 2003 Oxford University Press

Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps

João Aires-de-Sousa 1,* and Luisa Aires-de-Sousa 2

1 Departamento de Química, CQFB, campus Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Monte de Caparica
2 Clínica Universitária de Pediatria, Hospital de Santa Maria, Av. Prof. Egas Moniz, 1699 Lisboa Codex, Portugal

Received on May 29, 2002 ; revised on July 22, 2002 ; accepted on July 25, 2002

Motivation: We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence. This is a compact representation of the neighbourhood of a base. The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code). It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques.

Results: To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G. It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions. For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second). Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment.

Availability: Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep

Contact: jas{at}fct.unl.pt

Supplementary Information: Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002

* To whom correspondence should be addressed.


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