Michal Nanasi, Tomas Vinar, Brona Brejova. Probabilistic Approaches to Alignment with Tandem Repeats. In Aaron Darling, Jens Stoye, ed., Algorithms in Bioinformatics (WABI), 8126 volume of Lecture Notes in Computer Science, pp. 287-299, August 2013. Springer.

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Download from publisher: http://dx.doi.org/10.1007/978-3-642-40453-5_22

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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.

Last update: 10/10/2013