Publication details

Michal Nánási, Tomáš Vinař, Broňa Brejová. Probabilistic Approaches to Alignment with Tandem Repeats. In Aaron Darling, Jens Stoye, ed., Algorithms in Bioinformatics, 13th International Workshop (WABI), 8126 volume of Lecture Notes in Computer Science, pp. 287-299 , 2013. Springer.
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Abstract

We propose a simple tractable pair hidden Markov model for pairwise
sequence alignment that accounts for the presence of short tandem
repeats. Using the framework of gain functions, we design several
optimization criteria for decoding this model and describe the
resulting decoding algorithms, ranging from the traditional Viterbi
and posterior decoding to block-based decoding algorithms specialized
for our model. We compare the accuracy of individual decoding
algorithms on simulated data and find our approach superior to the
classical three-state pair HMM in simulations.