Re^3: Search for identical substrings


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Re^3: Search for identical substrings

by graff (Chancellor)

on Aug 18, 2005 at 18:54 UTC ( [id://484927]=note: print w/replies, xml )

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in reply to Re^2: Search for identical substrings
in thread Search for identical substrings

So, just to see if I understand the task... given those four (truncated?) lines of input data, would the following be the "right" answer?

LCS for 0 :: 1 = |ATGGAGAACATCACATCA|
LCS for 0 :: 2 = |TCACATCAGGACTCCTAGGACC|
LCS for 0 :: 3 = |CATCAC|
LCS for 1 :: 2 = |ACTCCTAGGACC|
LCS for 1 :: 3 = |CATCAC|
LCS for 2 :: 3 = |CAGGA|
[download]

This doesn't keep track of the actual index offsets where the longest match actually starts in each string for each pairwise comparison, but that would be easy to add.

That's the output from the code posted in my later reply in this thread, given those four lines of sample data as input.

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Re^4: Search for identical substrings by bioMan (Beadle) on Aug 19, 2005 at 16:38 UTC
Unfortunately my data doesn't give simple answers, and that is my fault completely for not being more careful with how I constructed the test data. My results are: `0 :: 1 ATGGAGAACATCACATCA and GACTCCTAGGACCCCTTC 0 :: 2 TCACATCAGGACTCCTAGGACC 0 :: 3 ACATCAC 1 :: 2 GACTCCTAGGACC 1 :: 3 ACATCAC 2 :: 3 CAGGA and ACAGG` [download]	[reply] [d/l]
Re^4: Search for identical substrings by bioMan (Beadle) on Aug 19, 2005 at 16:43 UTC
Unfortunately, the answers are not simple and that's my fault for not being more careful with the test data I created. The correct answers are: `0 :: 1 ATGGAGAACATCACATCA and GACTCCTAGGACCCCTTC 0 :: 2 TCACATCAGGACTCCTAGGACC 0 :: 3 ACATCAC 1 :: 2 GACTCCTAGGACC 1 :: 3 ACATCAC 2 :: 3 CAGGA and ACAGG` [download]	[reply] [d/l]

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