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In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings. Moreover, using our methodology, we show that indel parameters substantially vary between three genomic data sets: Mammals, bacteria, and retroviruses. Finally, we demonstrate how our methodology can be used to simulate MSAs based on indel parameters inferred from real data sets.
- Levy Karin, Eli (Author)
- Rabin, Avigayel (Author)
- Ashkenazy, Haim (Author)
- Shkedy, Dafna (Author)
- Avram, Oren (Author)
- Cartwright, Reed (Author)
- Pupko, Tal (Author)
- Biodesign Institute (Contributor)
Karin, E. L., Rabin, A., Ashkenazy, H., Shkedy, D., Avram, O., Cartwright, R. A., & Pupko, T. (2015). Inferring Indel Parameters using a Simulation-based Approach. Genome Biology and Evolution, 7(12), 3226-3238. doi:10.1093/gbe/evv212
- 2017-06-09 02:07:04
- 2021-12-03 02:10:14
- 2 years 4 months ago