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SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

Andy Pang1, Andrew D Smith3, Paulo AS Nuin1 and Elisabeth RM Tillier12*

Author Affiliations

1 Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada

2 Dept. Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

3 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA

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BMC Bioinformatics 2005, 6:236  doi:10.1186/1471-2105-6-236

Published: 27 September 2005

Abstract

Background

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.

Results

We have developed a new method of simulating protein sequence evolution, including insertion and deletion (indel) events in addition to amino-acid substitutions. The simulation generates both the simulated sequence family and a true sequence alignment that captures the evolutionary relationships between amino acids from different sequences. Our statistical model for indel evolution is based on the empirical indel distribution determined by Qian and Goldstein. We have parameterized this distribution so that it applies to sequences diverged by varying evolutionary times and generalized it to provide flexibility in simulation conditions. Our method uses a Monte-Carlo simulation strategy, and has been implemented in a C++ program named Simprot.

Conclusion

Simprot will be useful for testing methods of analysis of protein sequence families particularly alignment methods, phylogenetic tree building, detection of recombination and horizontal gene transfer, and homology detection, where knowing the true course of sequence evolution is essential.