Compute Position Weight Matrix, display SequenceLogo freq

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:ssss 1ssss 2ssss 3ssss 4ssss 5ssss 6ssss 7

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C :ssssssss 0.00ss 0.10ss 0.05ss 0.10ss 0.00ss 0.05ss 0.90

T :ssssssss 0.10ss 0.85ss 0.05ss 0.80ss 0.80ss 0.00ss 0.05

A :ssssssss 0.05ss 0.00ss 0.00ss 0.05ss 0.20ss 0.05ss 0.05

G :ssssssss 0.85ss 0.05ss 0.90ss 0.05ss 0.00ss 0.90ss 0.00

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H :ssssssss 0.75ss 0.75ss 0.57ss 1.02ss 0.72ss 0.57ss 0.57

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I :ssssssss 1.25ss 1.25ss 1.43ss 0.98ss 1.28ss 1.43ss 1.43

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Total I :ssssssss 9.05

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Mean I :ssssssss 1.29

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The consensus is GTGTTGC.

Note:

ssThe 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.

Thank you.

Regards,

Michael Chan JT