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 = '_____@gmail.com';
password = '_______';
recipientEmails = '____@_____';
---------- USAGE_MOTIFFINDING.M
---------- USAGE_MOTIFFINDING_MEMCONSTRAINEDVERSION.M
---------- USAGE_VITERBILIKEPROBABILISICMOTIFFINDING.M
=================================================================================
* 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: promethevx@yahoo.com.
Thank you.
Regards,
Michael Chan JT
인용 양식
Michael Chan (2024). Motif Finding (https://www.mathworks.com/matlabcentral/fileexchange/29362-motif-finding), MATLAB Central File Exchange. 검색됨 .
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