Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-10-27

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All times shown according to UTC.

Time Nick Message
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15:19 aef hi anyone here?
15:19 * rbuels waves at aef
15:19 aef hi, i'm not a perl writer and i never used bioperl
15:19 * rbuels picks up deafferret's arm and waves it
15:20 rbuels aef: you're in for an adventure then  ;-)
15:20 aef but i'm trying to understand something bioruby does
15:20 aef i bet bioperl is able to get the complement of a base sequence
15:21 rbuels i bet bioruby is too
15:21 aef if i want to get a complement of "gaatactcaagtc" in bioruby, i get "gacttgagtattc"
15:22 rbuels that's the *reverse* complement
15:22 rbuels which is the more common case
15:22 aef that means it has not only the complementary bases, but it is also inverted
15:22 rbuels yes, that's what people usually want.  it's called the reverse complement
15:22 aef but for translation, i need to reverse it again, right?
15:23 rbuels for translation, you just need to translate it.  there are methods for that
15:23 aef if i'm doing it manually, i would go from right to left, or not?
15:24 aef with a reverse complement
15:24 aef because the 5' end is on the right side
15:26 rbuels um, you could go right to left, or you could reverse the reverse complement and go left to right
15:27 aef ok, nice to know its right, so why do most people want the reverse complement?
15:27 rbuels because that's how you get the sequence of the complementary strand of a given piece of dna
15:28 rbuels dna has 2 strands stuck to eachother, and if you want to analyze one side and then the other, you do it frontways, and then on the reverse comp
15:30 aef i understand, thanks for your help
15:30 rbuels no prob
15:36 deafferret rbuels++ # so helpful
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