A novel, fast, HMM-with-Duration implementation – for application with a new, pattern recognition informed, nanopore detector

Table 2 As with Table 1, for all row entries the average dwell time of both the upper and lower signal levels increases proportionately with bin-count.

Bin #	2-state Geometric HMM	2n-state Explicit HMMwD	2-state Implicit HMMwD
10	720050	795723	741579
100	947062	957753	948505
1000	994978	995013	995005

Thus the resolution of the duration distribution for both the signal-generating and the signal-decoding HMM's are identical for all row entries. Upper and lower mean durations are .2 and .6 times that of the bin count, respectively. Upper and lower mean emissions are 50.0 and 45.0, respectively, whereas the emission variance for both upper and lower is 20.0. In other tests (see Fig. 7 and figures in the Additional Files), the decoding duration distribution is an increasingly refined step function approximation of the generating duration distribution. For the data shown in this table, both upper and lower durations are 3-component beta-mixtures with humps in the aggregate.

ISSN: 1471-2105