Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-26

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All times shown according to UTC.

Time Nick Message
06:12 Vein joined #bioperl
07:41 Cryonic joined #bioperl
09:14 faceface rbuels: distribution of sizes?
09:16 faceface also, there is nothing significant about SP6 T7 is there? i.e. there are no strand specific restriction sites taken into consideration when cloning a library of this size?
09:16 * faceface assumes not
09:30 faceface max I have == 315788 # LE_HBa0147G09
09:30 faceface min I have == 19252 # LE_HBa0040H21
09:30 faceface but those could be errors.
09:32 faceface mean = 137956.75
09:32 faceface (sample size 20)
12:29 kyanardag joined #bioperl
12:35 faceface mc buels!
12:35 faceface http://imagebin.ca/view/vQy_1Vq.html
12:36 faceface http://imagebin.ca/view/JWGfmc.html
12:36 faceface http://imagebin.ca/view/fts3oYmP.html
12:38 faceface I'm not sure, but I gess everything below 5000 is a problem
12:38 faceface possibly 50,000, but I don't know the library
12:39 * faceface wonders how to calculate 'compression statistics' on this scale
14:48 rbuels faceface: these histograms are distances between paired aligned bac ends?
17:02 faceface rbuels: yup
17:02 faceface for all tomato bes libs
17:02 xp_prg joined #bioperl
17:02 faceface and using a crummy alignment settings
17:03 faceface xp_prg: I use BioPerl to handle DNA sequences
17:04 rbuels xp_prg: i mostly use bioperl for handling seqs and processing annotations
17:05 rbuels xp_prg: but it's all a matter of what corner of bioinformatics you're in.
17:06 xp_prg handling dna sequences in what way if you will?
17:07 rbuels xp_prg: i don't do anything particularly complicated with sequences, mostly just reading them in and writing them out in fasta format, feeding them to various analysis tools (like blast, genomethreader, repeatmasker, etc)
17:08 rbuels xp_prg: faceface is probably more of a proper bioinformaticist than me ;-)
17:25 xp_prg tell me more about how you use blash, genomethreader, repeatmasker :>
17:26 xp_prg blash = blast
17:27 xp_prg I am trying to get a high level overview of how people are doing things with bioperl, I am going to teach a class
17:39 faceface rbuels: genomethreader?
17:40 faceface rbuels: is SP6 forward or reverse? (sorry for being lame)
17:40 faceface xp_prg: one use case... get the result of a sequene alignment - read in the alignments with BioPerl (no need to parse it, cus the standard formats have parsers written)
17:41 faceface print out all lenghts of the hits...
17:41 faceface (where identity > some threshold)
17:41 faceface xp_prg: its quite hacky really
17:41 faceface xp_prg: mostly format conversion is my main use of bioperl
17:43 xp_prg I wish I understood more of what you said
17:44 xp_prg but are you answering rbuels uses or your use?
18:13 rbuels faceface: SP6 is reverse.  genometheader is pretty much like exonerate.
20:35 veinous joined #bioperl
22:04 kyanardag joined #bioperl

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