Re^2: Filtering matches of near-perfect-matched DNA sequence pairs

Not_a_number, thank you for your response. Please see updated info in response to Anonymous_Monk's request for case examples. I hope the examples make it clearer. The "Text-Levenshtein" solution seems like it might work

Comment on Re^2: Filtering matches of near-perfect-matched DNA sequence pairs

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Re^3: Filtering matches of near-perfect-matched DNA sequence pairs by BrowserUk (Patriarch) on Mar 15, 2015 at 07:04 UTC
The "Text-Levenshtein" solution seems like it might work Whilst Levenshtein will work for your application, it is an exhaustive, and thus very slow O(n*m) algorithm. Even the XS version is many times slower than the xor method you use in the OP. As such, it is best avoided unless no other short-circuiting method can be found to solve your problem. The good news is that alternatives are nearly always possible. The only thing lacking here is a clear description of your data. If you would step back from your jargon and conceptual visualisation of the problem; and answer the multiple, impassioned pleas asking "what does your actual data look like?"; then I'm pretty sure you would have multiple, efficient, working solutions by now. With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". I'm with torvalds on this In the absence of evidence, opinion is indistinguishable from prejudice. Agile (and TDD) debunked	[reply]

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Re^3: Filtering matches of near-perfect-matched DNA sequence pairs
by BrowserUk (Patriarch) on Mar 15, 2015 at 07:04 UTC

The "Text-Levenshtein" solution seems like it might work

Whilst Levenshtein will work for your application, it is an exhaustive, and thus very slow O(n*m) algorithm.

Even the XS version is many times slower than the xor method you use in the OP. As such, it is best avoided unless no other short-circuiting method can be found to solve your problem.

The good news is that alternatives are nearly always possible. The only thing lacking here is a clear description of your data.

If you would step back from your jargon and conceptual visualisation of the problem; and answer the multiple, impassioned pleas asking "what does your actual data look like?"; then I'm pretty sure you would have multiple, efficient, working solutions by now.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority". I'm with torvalds on this

In the absence of evidence, opinion is indistinguishable from prejudice. Agile (and TDD) debunked

[reply]