Motif Finding 1.0

main executing reference usage: operationMain.m---------------------------------------------------------------------------------======= Demo 1 : Combinatorial motif finding =======[Demo a] : Sample-based motif findingusage_MotifFinding.m % mode 1usage_MotifFinding_MemConstrainedVersion.m[Demo b] : Probalisitic motif findingusage_MotifFinding.m % mode 2usage_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.---------------------------------------------------------------------------------[Demo 2] : Viterbi Probalisiticusage_ViterbiLikeProbabilisicMotifFinding.mThe objective is to illustrate Viterbi Probalisitic motif finding.---------------------------------------------------------------------------------[Demo 3]:usage_MotifFinding.m % mode [1 for Sample-based motif finding; 2 for Probalisitic motif finding]usage_MotifFinding_MemConstrainedVersion.mtargetFile = 'outputFile_MotifLen7.txt';% targetFile = 'outputFile_MotifLen11.txt';- To re-generates 2 files: outputFile_MotifLen7.txt and outputFile_MotifLen11.txtUncomment 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);---------------------------------------------------------------------------------=================================================================================* 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.

Requirements:	No special requirements
Platforms:	Matlab
Keyword:	3f3f3f,  Candidate,  Error,  Exceptions,  Memory,  Options,  Pattern,  Processing,  Seqused
Users rating:	0/10