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Code covered by the BSD License

DisplayModel(M, L, iterations... Display the HMM described by M, the log likelihood value,
ForBackF(M,Y) Forward-backward algorithm for step-HMM
ForwardBackward_3(M,Y,I0,test... function [LL newM gamma] = ForwardBackward_3(M,Y,I0,test,BigB)
M=MakeMonotonicModel(nu, yQua... function M=MakeMonotonicModel(nu, yQuantum, noiseSigma, transProb, stepSizes, stepSigma)
ModelChange(M1,M0) Check the changes in the transition probabilities. Looks at the
PlotAndLabelPeaks(x,y,minsize... function PlotAndLabelPeaks(x,y,minsize,xscale)
RestorationPlot(Y, EstY, wrap... function RestorationPlot(Y, EstY, wrap, yquantum, EYbase,markerstr) Fancy
WtConvol(a,b,m)
[EstY EstI LP Wrap]=ViterbiRe... % Viterbi algorithm for step-HMM
[X,Y]=StepSimulator(M,N) function [X,Y]=StepSimulator(M,N)
[X,Y]=StepSimulatorC(M,N) Given the number of time points N and the model M, simulate a staircase
[sigma nu]=EstSigmaAndNu(Y,I0) Find reasonable values for these variables based on the step data vector
b=Makeb(nu,sigma,DutyCycle,Er...
ms=QuickShift(m,shift) Faster replacement for circshift for time-critical applications.
ms=QuickShiftMex(m,shift) Faster replacement for circshift for time-critical applications.
n=NextNiceNumber(x,f) function n=NextNiceNumber(x)
xs=Step125(x)
MotorHMM1.m
MotorHMM2.m
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3.0 | 1 rating Rate this file 19 Downloads (last 30 days) File Size: 792.17 KB File ID: #24697

Hidden Markov Models for Molecular Motors

11 Jul 2009 (Updated 09 Nov 2011)

A set of functions for analysing noisy recordings of the random stepping of molecular motors

File Information
Description	Hidden Markov models are used to describe the "stepping" behavior of molecular motors, as measured by single-molecule fluorescence techniques. Our HMM implementation is described in two 2010 papers by F. Müllner, S. Syed, P. Selvin and F. Sigworth, Biophysical J. 99:3684-3695 and 3696-3702. Meanwhile a readme file and example script demonstrate the use of the functions.
Required Products	MATLAB
MATLAB release	MATLAB 7.8 (R2009a)
Other requirements	MEX file sources are included for acceleration of the functions, but are not strictly required.

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Everyone's Tags	biophysics, fluorescence, hidden markov, markov model, physics, signal processing, single molecule, statistics, step detector
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Comments and Ratings (1)
02 Jan 2010	saurabh bhardwaj	excellent file , must read for researchers

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Updates
23 Mar 2010	Updated version with a second example script and correction to the MAP estimation code.
09 Nov 2011	Removed .mex files. Added citation of published papers describing the algorithms.