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q-bio.QM2021
Probabilistic Models of k-mer Frequencies (Extended Abstract)
Askar Gafurov, Tomáš Vinař, Broňa Brejová
In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abun…
q-bio.QM2013
Probabilistic Approaches to Alignment with Tandem Repeats
Michal Nánási, Tomáš Vinař, Broňa Brejová
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…