Detecting fuzzy amino acid tandem repeats in protein sequences

Authors:
Marco Pellegrini;M. Elena Renda;Alessio Vecchio
Affiliations:
Istituto di Informatica e Telematica, Pisa, Italy;Istituto di Informatica e Telematica, Pisa, Italy;Università degli Studi di Pisa, Pisa, Italy
Venue:
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2011

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Abstract

Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence. In this paper we present PTRStalker, a new algorithm for ab-initio detection of very fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools.