You say lower down that "these are actually quite slow for even 10,000 comparisons".

  1. How long?
  2. How many comparisons?

    Is the time you've (hopefully) supplied, for comparing each of the 10,000 sequences against one target string (ie. 10,000 compares)?

    Or each of the 10,000 against each of the other 9,999 (ie. 50 million compares)?

  3. How long are the sequences you are dealing with?

I have a routine that will cross-compare 10,000 x 8-char sequences (50e6 comparisons) in 246 seconds. And 10,000 x 16-chars sequences in a little under 500 seconds. How does that compare to your current method?

To put that in perspective, if your "actually quite slow" is for 10,000 compares against a single target, then I can do that in 0.05 seconds.

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".
In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

In reply to Re: mismatching characters in dna sequence by BrowserUk
in thread mismatching characters in dna sequence by prbndr

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