Compute Position Weight Matrix (PWM) and display SequenceLogo in terms of frequency

Illustrates computation of best match scoring with PWM and constructs sequence logo.

main executing reference usage: operationMain.m
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main executing reference usage: usage_PWM.m
[Demo 1]: PWM (Position Weight Matrix) and Information Content
usage_PWM.m

The objective is to compute the PWM, and report the consensus.

Sample output:

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String index: 1 2 3 4 5 6 7
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C : 0.00 0.10 0.05 0.10 0.00 0.05 0.90
T : 0.10 0.85 0.05 0.80 0.80 0.00 0.05
A : 0.05 0.00 0.00 0.05 0.20 0.05 0.05
G : 0.85 0.05 0.90 0.05 0.00 0.90 0.00
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H : 0.75 0.75 0.57 1.02 0.72 0.57 0.57
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I : 1.25 1.25 1.43 0.98 1.28 1.43 1.43
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Total I : 9.05
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Mean I : 1.29
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The consensus is GTGTTGC.

Note:
The sequencelogo feature does not use the bioinformatics toolbox.

Caveat: The y-axis of the sequencelogo is in terms of frequency. It is not perfect, but it serves as a basic visual guide in the absence of having the seqlogo inbuilt.
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main executing reference usage: usage_computeProbabilityOfSequenceGivenPWM.m
[Demo 2]: Best Matches on PWM
usage_computeProbabilityOfSequenceGivenPWM.m

The objective is to illustrate Best Matches on PWM with determination of locations.

* To verify results, save results in targetFile and run usage_PWM.m with
targetFile = 'inputFromBestMatchFromDemo2.txt';
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* Caveat: For educational reference only.

If the reference demo has a more elegant presentation, please do not hesitate to suggest and send feedback to author.
Email: [e-mail].

Thank you.

Regards,
Michael Chan JT