Motif Finding

Illustrates Combinatorial and Viterbi-akin motif finding.

main executing reference usage: operationMain.m
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======= Demo 1 : Combinatorial motif finding =======
[Demo a] : Sample-based motif finding
usage_MotifFinding.m % mode 1
usage_MotifFinding_MemConstrainedVersion.m

[Demo b] : Probalisitic motif finding
usage_MotifFinding.m % mode 2
usage_MotifFinding_MemConstrainedVersion.m

- set mode [1 for Sample-based motif finding; 2 for Probalisitic motif finding]

The objective is to illustrate Combinatorial motif finding.

* Caveat: It is recommended to use usage_MotifFinding_MemConstrainedVersion.m, as it caters for memory constraints.
For instance, k = 9, there are 262144, ie. 4^9, permutations to test. This subjects the computer to run off of memory very easily under more than a quarter of million runs.

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[Demo 2] : Viterbi Probalisitic
usage_ViterbiLikeProbabilisicMotifFinding.m

The objective is to illustrate Viterbi Probalisitic motif finding.

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[Demo 3]:
usage_MotifFinding.m % mode [1 for Sample-based motif finding; 2 for Probalisitic motif finding]
usage_MotifFinding_MemConstrainedVersion.m
targetFile = 'outputFile_MotifLen7.txt';
% targetFile = 'outputFile_MotifLen11.txt';

- To re-generates 2 files: outputFile_MotifLen7.txt and outputFile_MotifLen11.txt
Uncomment the following lines. Note that each generation produces different data sets.
% system('run_motifGen.jar.bat');
- set mode [1 for Sample-based motif finding; 2 for Probalisitic motif finding]

* Caveat:
- As jar files are not allowed on Matlab Central, please send an email request to the author, if this is required.
- Limitations on k = 11. The permutations itself may run out of memory.

Sample exceptions:
Processing pattern motif candidate #9634
??? Out of memory. Type HELP MEMORY for your options.

Error in ==> usage_sampleBasedMotifFinding at 60
hammingDistScore(j,1:numberOfHammingScoresToBeComputed, i) =
hammingDistanceOfpatternAgainst1Sequence( seqUsed,
patternUsed);

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* Caveat: The sender's email has to be a gmail account to send the results via email.
Exhaustive mode may take around > 2 hours for k = 9.

For automated results emailing, please provide the following parameters in the stated files:

senderMail = '[e-mail]';
password = '_______';
recipientEmails = '____@_____';

---------- USAGE_MOTIFFINDING.M
---------- USAGE_MOTIFFINDING_MEMCONSTRAINEDVERSION.M
---------- USAGE_VITERBILIKEPROBABILISICMOTIFFINDING.M
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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