Distributed toggle clusters learning
New!
Here we implement distributed toggle clustering and classification of nanopore
DNA hairpin toggles based on mixtures of HMM profiles. This approach is discussed
in our recently submitted paper:
Alexander Churbanov and Stephen Winters-Hilt, Clustering ionic flow blockade toggles with Mixture of
HMMs, BMC Bioinformatics, 2008, MCBIOS V proceedings.
- Here is the preliminary report on our approach slides
- Corrected Figure 4 from the manuscript
- Demo program
Duration learning demo
New!
This program demonstrates the duration learning for the nanopore ionic
flow blockade signal as described in our recent article
Alexander Churbanov, Carl Baribault and Stephen Winters-Hilt, Duration learning for analysis of
nanopore ionic current blockades, BMC Bioinformatics, 8(2007), Suppl. 7.
- The corect picture for the profile shown on page 6 in Figure 4 could be seen here.
- Demo program
Linear memory HMM demo
New!
We managed to improve originally proposed linear memory implementation of Baum-Welch
and Viterbi decoding for HMM as discussed in article by
István Miklós and Irmtraud M. Meyer.
CSB2007 PM1 tutorial session
Here are the lecture slides describing the
concepts of probabilistic modelling we use in our research.
Lecture on splicing
Here are the lecture slides describing the concept of Homology
based gene structural prediction, Ab initio gene finding and splice site
sensor design program.
Lecture on linear memory HMM
Here are the slides on our linear memory HMM implementation experiments.
Progress report on distributed toggle clustering with MHMM
Here are the slides on clustering with Mixture of HMM profiles.
We have already run the algorithm in distributed manner using Java RMI.
|
 |