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Okay, but I'm not sure whether you can safetly discount the possibility of long sequences of repeated characters, even in biodata. The following shows a scan of the complete drosophila (fruit fly) genome looking for sequences of repeated DNA characters:

>perl -nlwe" print $1 while m[((.)\2+)]g" na_clones.dros.RELEASE2.5 | +( More? perl -nle"$b{ length($_) }{ chop $_}++ } { printf qq[length %d :[ A:%d C:%d G:%d T:%d ]\n], $_, @{$b{$_}}{'A','C','G','T'} for sort{$b<=>$a} keys %b" ) length 50 :[ A:1 C:0 G:0 T:0 ] length 47 :[ A:1 C:0 G:0 T:0 ] length 45 :[ A:1 C:0 G:0 T:0 ] length 44 :[ A:0 C:0 G:0 T:0 ] length 43 :[ A:0 C:0 G:0 T:1 ] length 42 :[ A:1 C:0 G:0 T:0 ] length 41 :[ A:1 C:0 G:0 T:1 ] length 40 :[ A:1 C:0 G:0 T:0 ] length 39 :[ A:0 C:0 G:0 T:0 ] length 38 :[ A:1 C:0 G:0 T:0 ] length 37 :[ A:2 C:0 G:0 T:0 ] length 36 :[ A:5 C:0 G:0 T:4 ] length 35 :[ A:5 C:0 G:0 T:3 ] length 34 :[ A:2 C:0 G:0 T:3 ] length 33 :[ A:2 C:0 G:0 T:3 ] length 32 :[ A:1 C:0 G:0 T:1 ] length 31 :[ A:5 C:0 G:0 T:5 ] length 30 :[ A:4 C:0 G:0 T:5 ] length 29 :[ A:10 C:0 G:0 T:6 ] length 28 :[ A:12 C:0 G:0 T:13 ] length 27 :[ A:19 C:0 G:0 T:12 ] length 26 :[ A:26 C:0 G:0 T:28 ] length 25 :[ A:35 C:1 G:1 T:34 ] length 24 :[ A:48 C:0 G:0 T:47 ] length 23 :[ A:63 C:0 G:1 T:59 ] length 22 :[ A:78 C:1 G:0 T:84 ] length 21 :[ A:109 C:5 G:3 T:91 ] length 20 :[ A:126 C:5 G:6 T:144 ] length 19 :[ A:188 C:17 G:15 T:148 ] length 18 :[ A:240 C:25 G:26 T:314 ] length 17 :[ A:411 C:45 G:55 T:389 ] length 16 :[ A:647 C:73 G:78 T:656 ] length 15 :[ A:905 C:122 G:133 T:886 ] length 14 :[ A:1267 C:191 G:216 T:1208 ] length 13 :[ A:1813 C:255 G:260 T:1805 ] length 12 :[ A:2702 C:353 G:353 T:2800 ] length 11 :[ A:4209 C:380 G:404 T:4184 ] length 10 :[ A:7181 C:446 G:428 T:7343 ] length 9 :[ A:9964 C:386 G:437 T:10011 ] length 8 :[ A:14581 C:699 G:601 T:14514 ] length 7 :[ A:28336 C:2656 G:2644 T:28782 ] length 6 :[ A:90274 C:11644 G:11543 T:89663 ] length 5 :[ A:308601 C:52038 G:52017 T:309011 ] length 4 :[ A:889188 C:199827 G:200919 T:885567 ] length 3 :[ A:2424590 C:938297 G:935629 T:2422964 ] length 2 :[ A:6232754 C:4721693 G:4718156 T:6219367 ]

As you can see, at lengths over 16, they are still a fairly frequent occurence. And even at lengths > 32, there are still enough to be worrying.


Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?
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In reply to Re^3: Fast common substring matching by BrowserUk
in thread Fast common substring matching by GrandFather

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