Problem 939. DNA Pattern Match: Performance Metric - Speed

Created by Richard Zapor

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{"relationships":[{"relationshipType":"http://schemas.mathworks.com/matlab/code/2013/relationships/document","targetMode":"","relationshipId":"rId1","target":"/matlab/document.xml"},{"relationshipType":"http://schemas.mathworks.com/matlab/code/2013/relationships/output","targetMode":"","relationshipId":"rId2","target":"/matlab/output.xml"}],"parts":[{"partUri":"/matlab/document.xml","relationship":[],"contentType":"application/vnd.mathworks.matlab.code.document+xml","content":"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<w:document xmlns:w=\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\"><w:body><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>The Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>At</w:t></w:r><w:r><w:t> </w:t></w:r><w:hyperlink w:docLocation=\"http://imacst.com/issues/volume-3issue-1/\"><w:r><w:t>IMACST</w:t></w:r></w:hyperlink><w:r><w:t> the paper</w:t></w:r><w:r><w:t> </w:t></w:r><w:hyperlink w:docLocation=\"http://imacst.com/web_documents/1202002.pdf\"><w:r><w:t>An Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern</w:t></w:r></w:hyperlink><w:r><w:t> claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>Matlab can achieve matching a six pattern set of L=6 in &lt;15 msec (i5/16GB). This is merely a 99.8% time reduction.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:rPr><w:b/></w:rPr><w:t>Challenge Description:</w:t></w:r><w:r><w:t> DNA is made of letters ACGT,</w:t></w:r><w:r><w:t> </w:t></w:r><w:hyperlink w:docLocation=\"http://en.wikipedia.org/wiki/DNA\"><w:r><w:t>wiki DNA</w:t></w:r></w:hyperlink><w:r><w:t>, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:rPr><w:b/></w:rPr><w:t>Input:</w:t></w:r><w:r><w:t> [DNA, DNA_ID, Patterns]</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>DNA is a 1.8M long uint8 row vector of values 0 thru 3.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>DNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>Patterns is an Nx6 uint8 array where each row corresponds to a search pattern.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:rPr><w:b/></w:rPr><w:t>Output:</w:t></w:r><w:r><w:t> Locations</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>Locations of all start indices that match any of the patterns</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:rPr><w:b/></w:rPr><w:t>Scoring:</w:t></w:r><w:r><w:t> Average Time (msec) for a block of L=6 patterns</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>Example:</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>DNA= [0 1 2 3 3 2 1 0 1 2 3 3]</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>Pattern = [2 3 3 2 1 0]</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>Locations = [3]</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:rPr><w:b/></w:rPr><w:t>Hints:</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>Vectorization (Base 4 to Base 10 of 6 character words)</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>Bitshift/Reshape to create all words</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"ListParagraph\"/><w:numPr><w:numId w:val=\"1\"/></w:numPr></w:pPr><w:r><w:t>Logical Indexing</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>Coming soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza</w:t></w:r></w:p></w:body></w:document>"},{"partUri":"/matlab/output.xml","contentType":"text/xml","content":"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\" ?><embeddedOutputs><metaData><evaluationState>manual</evaluationState><layoutState>code</layoutState><outputStatus>ready</outputStatus></metaData><outputArray type=\"array\"/><regionArray type=\"array\"/></embeddedOutputs>"}]}

The Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.At <a href="http://imacst.com/issues/volume-3issue-1/">IMACST</a> the paper <a href="http://imacst.com/web_documents/1202002.pdf">An Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern</a> claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.Matlab can achieve matching a six pattern set of L=6 in &lt;15 msec (i5/16GB). This is merely a 99.8% time reduction.Challenge Description:
DNA is made of letters ACGT, <a href="http://en.wikipedia.org/wiki/DNA">wiki DNA</a>, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)Input: [DNA, DNA_ID, Patterns]<ul><li>DNA is a 1.8M long uint8 row vector of values 0 thru 3.</li><li>DNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.</li><li>Patterns is an Nx6 uint8 array where each row corresponds to a search pattern.</li></ul>Output: LocationsLocations of all start indices that match any of the patternsScoring: Average Time (msec) for a block of L=6 patternsExample:<ul><li>DNA= [0 1 2 3 3 2 1 0 1 2 3 3]</li><li>Pattern = [2 3 3 2 1 0]</li><li>Locations = [3]</li></ul>Hints:<ul><li>Vectorization (Base 4 to Base 10 of 6 character words)</li><li>Bitshift/Reshape to create all words</li><li>Logical Indexing</li></ul>Coming soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza

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Problem 939. DNA Pattern Match: Performance Metric - Speed

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