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Published online 30 April 2004

Nucleic Acids Research, 2004, Vol. 32, No. 8 2464-2473
© 2004 Oxford University Press

Contact-based sequence alignment

Jens Kleinjung*, John Romein, Kuang Lin1 and Jaap Heringa

Bioinformatics Unit, Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1081A, 1081HV Amsterdam, The Netherlands and 1 Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK

*To whom correspondence should be addressed. Tel: +31 20 4447783; Fax: +31 20 4447653; Email: jkleinj{at}cs.vu.nl

Received March 15, 2004; Revised and Accepted April 5, 2004

This paper introduces the novel method of contact-based protein sequence alignment, where structural information in the form of contact mutation probabilities is incorporated into an alignment routine using contact-mutation matrices (CAO: Contact Accepted mutatiOn). The contact-based alignment routine optimizes the score of matched contacts, which involves four (two per contact) instead of two residues per match in pairwise alignments. The first contact refers to a real side-chain contact in a template sequence with known structure, and the second contact is the equivalent putative contact of a homologous query sequence with unknown structure. An algorithm has been devised to perform a pairwise sequence alignment based on contact information. The contact scores were combined with PAM-type (Point Accepted Mutation) substitution scores after parameterization of gap penalties and score weights by means of a genetic algorithm. We show that owing to the structural information contained in the CAO matrices, significantly improved alignments of distantly related sequences can be obtained. This has allowed us to annotate eight putative Drosophila IGF sequences. Contact-based sequence alignment should therefore prove useful in comparative modelling and fold recognition.


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