Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-09-01

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Time Nick Message
00:00 kyanardag_ joined #bioperl
00:04 xp_prg anyone know a way to tell if primer3 primers have hairpins in them?
00:05 rbuels hmmmmm
00:05 rbuels don't think hairpins in primer pairs are usually a problem, because of the temps they run PCRs at
00:06 xp_prg so you don't know a way to do it?
00:06 rbuels but having never actually done any wet lab work myself, i'm probably full of it
00:06 rbuels xp_prg: didn't say that.
00:06 rbuels lol
00:06 rbuels probably if you aligned the primer against a reverse complement of itself?
00:06 rbuels and looked for strong matches?
00:07 rbuels you could use BLAST (apt-get install blastall), probably
00:08 xp_prg ok cool
00:08 rbuels to get a reverse complement you can use the revcom() method on a Bio::Seq
00:08 xp_prg I don't understand how having a reverse compliment helps me with this problem
00:08 rbuels oh wait...not the reverse compliment
00:08 rbuels just the reverse
00:09 xp_prg don't understand how the reverse helps either
00:09 rbuels xp_prg: well a hairpin can form when a molecule sticks to itself right?
00:10 rbuels so......
00:10 rbuels wait it's not the reverse either..
00:10 * rbuels thinks a little more
00:11 xp_prg no a hairpin is usually a cell receptor and has hydrophobic molecules and is shaped like a hairpin
00:11 xp_prg if a primer is a hairpin it will disrupt the transcription of the protein
00:12 rbuels never heard of that kind of hairpin
00:12 rbuels well...actually yeah that makes sense....
00:12 rbuels the hairpin conformation would screw up transcription
00:13 rbuels but the hairpin forms because of certain properties that primer's nucleotides have in relation to eachother, right?
00:13 xp_prg don't know what else to tell you that I have told you
00:14 rbuels yeah.....so to detect possible hairpin conformations you would find where one part of the primer would be the reverse complement of itself...
00:15 rbuels i think.
00:16 xp_prg its an actual melecular strucure
00:16 xp_prg with hydrophobic probperties, dong what you said doesn't address that in any way I think
00:17 rbuels this is what you're talking about right? http://en.wikipedia.org/wiki/Stem-loop
00:18 rbuels cause that's what i was talking about
00:19 xp_prg http://www.premierbiosoft.com/te​ch_notes/PCR_Primer_Design.html
00:19 xp_prg it talks about it here
00:21 rbuels yeah those are the same thing.  intramolecular interaction of the primer with itself forming stem loops.
00:22 rbuels i don't know how to measure the delta-G of a given loop though
00:22 xp_prg oh cool, forgive me, I am not as versed as you :>
00:23 rbuels i would think that primer design programs would take all this stuff into account......
00:23 rbuels but i don't really know, since i've never done any primer design
00:24 rbuels yeah....looks like primer3 does anyway
00:27 rbuels xp_prg: if you're running a debian-based system, apt-get install primer3
00:27 rbuels zless  /usr/share/doc/primer3/README.txt.gz
00:27 rbuels search for string PRIMER_SELF_ANY
00:28 rbuels that's the primer3 input arg that tweaks some of the checking it does for this kind of thing
00:33 xp_prg thanks rbuels
00:34 rbuels xp_prg: no prob.  as you can tell, primer design is not by forte  ;-)
00:34 rbuels s/by/my/
00:34 xp_prg well always good to learn new things :>
00:34 xp_prg I am still confused what a primer does :>
00:36 rbuels http://upload.wikimedia.org/w​ikipedia/commons/8/87/PCR.svg
00:36 rbuels in the diagram, the primers are the red lines
00:37 rbuels little piece of dna that sticks to the other pieces, and provides a start for polymerase to build more dna
00:41 xp_prg hmm... interesting
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14:35 deafferret ooo! ooo! I know about primers!  :D
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