Beefy Boxes and Bandwidth Generously Provided by pair Networks
good chemistry is complicated,
and a little bit messy -LW
 
PerlMonks  

Comment on

( #3333=superdoc: print w/ replies, xml ) Need Help??

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?
"Science is about questioning the status quo. Questioning authority".
The "good enough" maybe good enough for the now, and perfection maybe unobtainable, but that should not preclude us from striving for perfection, when time, circumstance or desire allow.

In reply to Re^3: Fast common substring matching by BrowserUk
in thread Fast common substring matching by GrandFather

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":



  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • Outside of code tags, you may need to use entities for some characters:
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.
  • Log In?
    Username:
    Password:

    What's my password?
    Create A New User
    Chatterbox?
    and the web crawler heard nothing...

    How do I use this? | Other CB clients
    Other Users?
    Others studying the Monastery: (5)
    As of 2014-07-31 01:46 GMT
    Sections?
    Information?
    Find Nodes?
    Leftovers?
      Voting Booth?

      My favorite superfluous repetitious redundant duplicative phrase is:









      Results (244 votes), past polls