Problem 79. DNA N-Gram Distribution

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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>Given a string s and a number n, find the most frequently occurring n-gram in the string, where the n-grams can begin at any point in the string. This comes up in DNA analysis, where the 3-base reading frame for a codon can begin at any point in the sequence.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>So for</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"code\"/></w:pPr><w:r><w:t><![CDATA[ s = 'AACTGAACG']]></w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>and</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"code\"/></w:pPr><w:r><w:t><![CDATA[ n = 3]]></w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>we get the following n-grams (trigrams):</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"code\"/></w:pPr><w:r><w:t><![CDATA[ AAC, ACT, CTG, TGA, GAA, AAC, ACG]]></w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:t>Since AAC appears twice, then the answer, hifreq, is AAC. There will always be exactly one highest frequency n-gram.</w:t></w:r></w:p><w:p><w:pPr><w:pStyle w:val=\"text\"/></w:pPr><w:r><w:rPr><w:i/></w:rPr><w:t>This problem was originally inspired by a</w:t></w:r><w:r><w:rPr><w:i/></w:rPr><w:t> </w:t></w:r><w:hyperlink w:docLocation=\"http://www.mathworks.com/matlabcentral/newsreader/view_thread/278173\"><w:r><w:rPr><w:i/></w:rPr><w:t>MATLAB Newsgroup discussion</w:t></w:r></w:hyperlink><w:r><w:rPr><w:i/></w:rPr><w:t>.</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>"}]}

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E Chang on 22 Oct 2018

It should be noted that spaces should be ignored or else test suites 3 and 5 fail.

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Problem 79. DNA N-Gram Distribution

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