Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number
of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone modfications at the boundaries.
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.
