Common DNA Subsequence of Genes

The Version 7 functions LongestCommonSequence and LongestCommonSubsequence are now supplemented by their positional counterparts LongestCommonSequencePositions and LongestCommonSubsequencePositions.

Compare the DNA sequences of random genes of the Y chromosome.

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genes = RandomSample[GenomeData["ChromosomeYGenes"], 4]

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Group these genes by pairs.

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With[{subsets = Subsets[genes, {2}]}, Table[pair[i] = subsets[[i]], {i, 1, Length[subsets]}]];

Define a function that will get the positions of the longest continuous DNA sequence common to each pair, together with the sequence itself.

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commonDNASubequence[{g1_, g2_}] := With[{d1 = GenomeData[g1], d2 = GenomeData[g2]}, {{g1, g2}, LongestCommonSubsequencePositions[d1, d2], LongestCommonSubsequence[d1, d2]}]

Longest common subsequence of the first pair.

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commonDNASubequence[pair[1]]

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Longest common subsequence of the second pair.

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commonDNASubequence[pair[2]]

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Longest common subsequence of the third pair.

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commonDNASubequence[pair[3]]

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Longest common subsequence of the fourth pair.

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commonDNASubequence[pair[4]]

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Longest common subsequence of the fifth pair.

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commonDNASubequence[pair[5]]

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Longest common subsequence of the sixth pair.

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commonDNASubequence[pair[6]]

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