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Re^6: Longest common substring with N mismatches

by Anonymous Monk
on Sep 11, 2017 at 17:09 UTC ( #1199137=note: print w/replies, xml ) Need Help??


in reply to Re^5: Longest common substring with N mismatches
in thread Longest common substring with N mismatches

Sorry, I meant to write k-mer before :)
One example could be the following (using also the node you mentioned as input):
$str1='AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'; $str2='RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAABAAAAAAAAAAAAAAAAAAAAAAAABAAZZZZZZZ';

In this case, the whole $str1 should much because it only has 1 mismatch (assuming the user sets the allowed #mismatches to 1) and not only the AAAAA before the B.

Replies are listed 'Best First'.
Re^7: Longest common substring with N mismatches
by LanX (Bishop) on Sep 11, 2017 at 17:17 UTC
    Looks like the same solution fits, xor both strings at different positions and count the longest runs of zeros tolerating n non zeros in between, probably with a composed regex.

    See ^ in perlop#Bitwise-Or-and-Exclusive-Or

    Cheers Rolf
    (addicted to the Perl Programming Language and ☆☆☆☆ :)
    Je suis Charlie!

Re^7: Longest common substring with N mismatches
by Anonymous Monk on Sep 11, 2017 at 17:14 UTC

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