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(jeffa) Re: Finding DNA string mismatches

by jeffa (Bishop)
on Apr 22, 2003 at 14:31 UTC ( #252272=note: print w/replies, xml ) Need Help??


in reply to Finding DNA string mismatches

Hi. This is not an answer. I just wanted to comment that there is a CPAN module (or rather a suite of them) called bioperl (there is even a website). I am always curious why i see lots of questions like this, but no recommendations to use bioperl. I can say for the record that i have tinkered with bioperl just a bit, and it is very complex (as this pdf file can attest). However, if i were doing DNA comparisons and such on a regular basis, i would most certainly put aside some time to learn how to use bioperl instead of rolling my own solutions. At least until i had a good feel for it.

jeffa

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)
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Re: (jeffa) Re: Finding DNA string mismatches
by BrowserUk (Patriarch) on Apr 22, 2003 at 22:16 UTC

    Given the regularity with which this problem comes uparound here, I concluded that this problem is used as a sample question for those learning to use perl in the Bioinformatics field.

    I have this mental picture of a lecturer somewhere (or several somewheres:), giving the question out as homework, running through the myriad variations of regex and substr solutions that result and then writing 3 lines of perl (including use Bioperl;) to demonstrate the "right way" to do it:).

    As problems go, it is a nice, clean, self-contained, real-world problem with a million possible solutions just ideal for teaching purposes.


    Examine what is said, not who speaks.
    1) When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong.
    2) The only way of discovering the limits of the possible is to venture a little way past them into the impossible
    3) Any sufficiently advanced technology is indistinguishable from magic.
    Arthur C. Clarke.

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