Reverse translations of gene-coding DNA sequences using hidden Markov models

Tomasz Kaczynski; Robert Nowak

doi:10.1117/12.2000163

15 October 2012 Reverse translations of gene-coding DNA sequences using hidden Markov models

Tomasz Kaczynski, Robert Nowak

Proceedings Volume 8454, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2012; 84541P (2012) https://doi.org/10.1117/12.2000163
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2012, 2012, Wilga, Poland

Abstract

This work is aimed to algorithmically (in silico) reproduce the sequence of DNA from protein sequence, i.e. solve protein back-translation problem or reverse translation problem. Presented solution produces a result using hidden Markov models without usage of codon frequency data obtained in other (previous) analysis. Based on biological foundations of protein biosynthesis the Markov model is constructed, then trained with the support of the Viterbi algorithm, and used to estimate the most likely coding sequence. An application that implements the above algorithm is described, the results obtained by this application are studied, and comparison to other solutions of the protein back-translation (reverse translation) problem is presented.

Citation Download Citation

Tomasz Kaczynski and Robert Nowak "Reverse translations of gene-coding DNA sequences using hidden Markov models", Proc. SPIE 8454, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2012, 84541P (15 October 2012); https://doi.org/10.1117/12.2000163

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