Comparative genomics on artificial life. (English) Zbl 1478.92129
Beckmann, Arnold (ed.) et al., Pursuit of the universal. 12th conference on computability in Europe, CiE 2016, Paris, France, June 27 – July 1, 2016. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 9709, 35-44 (2016).
Summary: Molecular evolutionary methods and tools are difficult to validate as we have almost no direct access to ancient molecules. Inference methods may be tested with simulated data, producing full scenarios they can be compared with. But often simulations design is concomitant with the design of a particular method, developed by a same team, based on the same assumptions, when both should be blind to each other. In silico experimental evolution consists in evolving digital organisms with the aim of testing or discovering complex evolutionary processes. Models were not designed with a particular inference method in mind, only with basic biological principles. As such they provide a unique opportunity to blind test the behavior of inference methods. We give a proof of this concept on a comparative genomics problem: inferring the number of inversions separating two genomes. We use Aevol, an in silico experimental evolution platform, to produce benchmarks, and show that most combinatorial or statistical estimators of the number of inversions fail on this dataset while they were behaving perfectly on ad-hoc simulations. We argue that biological data is probably closer to the difficult situation.
For the entire collection see [Zbl 1337.68005].
For the entire collection see [Zbl 1337.68005].
MSC:
| 92D15 | Problems related to evolution |
| 92D10 | Genetics and epigenetics |
| 92B20 | Neural networks for/in biological studies, artificial life and related topics |
| 92-08 | Computational methods for problems pertaining to biology |
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