00:15:07 *** conley has quit (Read error: 104 (Connection reset by peer)) 00:15:57 *** conley (n=ibcliffo@spode.cs.vt.edu) has joined #bioinformatics 00:16:14 *** conley has quit (Read error: 104 (Connection reset by peer)) 00:16:19 *** conley (n=ibcliffo@spode.cs.vt.edu) has joined #bioinformatics 00:26:53 *** Lynx (n=lynx@tina-10-4.genetik.uni-koeln.de) has joined #bioinformatics 00:33:53 Hrm. We have a full (as in complete) yeast mutation library in the attic. 00:34:04 Is this normal? 00:37:20 Hahah. 00:37:25 Who is Aciel? 00:43:35 *** Lynx_ has quit (Read error: 110 (Connection timed out)) 00:43:35 *** Lynx is now known as Lynx_ 01:43:22 *** kanzure has quit ("Leaving.") 03:22:34 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 03:39:26 *** svensko_ has quit (Remote closed the connection) 03:40:31 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 03:50:34 *** svensko_ has quit (Remote closed the connection) 04:03:52 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 04:06:36 *** svensko_ has quit (Remote closed the connection) 04:32:06 *** rogers (i=rogers@bling.bling.org) has joined #bioinformatics 04:34:35 *** synthasee (n=synthase@69.254.170.145) has joined #bioinformatics 04:40:05 *** highvoltz has quit (Remote closed the connection) 04:40:23 *** nordlicht (n=nordlich@141.53.70.85) has joined #bioinformatics 04:45:43 *** synthase has quit (Read error: 110 (Connection timed out)) 05:16:46 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 05:18:13 *** svensko_ has quit (Remote closed the connection) 05:19:45 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 05:20:16 *** svensko_ has quit (Remote closed the connection) 05:21:49 *** svensko_ (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 05:23:26 *** _dan has quit (Read error: 104 (Connection reset by peer)) 05:34:31 *** percent_ (n=percent@66.158.193.28) has joined #bioinformatics 06:01:59 *** percent_ has parted #bioinformatics () 06:10:50 *** synthasee has quit (Client Quit) 06:44:17 *** _dan (n=dan@shady.org) has joined #bioinformatics 07:23:21 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 10:02:55 *** toru has quit ("Ex-Chat") 10:08:51 *** rogers has quit () 10:41:56 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 11:00:47 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:12:57 *** nordlicht has quit ("Verlassend") 11:20:20 *** ybit has quit (Remote closed the connection) 11:57:01 *** kanzure (i=bryan@dhcp-146-6-213-183.icmb.utexas.edu) has joined #bioinformatics 12:03:42 faceface: I'll be sure to say hi to Wan Kim Que. 12:22:57 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 13:31:17 I'm still looking for some good bioinformatics papers of recent publications. Any recommendations? 13:37:04 kanzure: what topic? 13:37:12 Marcott [au]? 13:37:38 Yes 13:37:40 Just looking for stuff 13:37:59 * kanzure goes 13:38:52 where? 13:39:18 <_dan> remember if you leave the terminal.. you cease to exist! 13:39:25 hrm... you reminded me how little I am reading lately... 13:39:43 <_dan> do abstracts count as reading? 13:39:50 I have the idea in my head that I can think of some exciting recent papers, but when I try... I come up blanck... like I hypnotized myself... 13:39:56 do reviews count as reading? 13:40:04 <_dan> they had better 13:40:21 I must have some papers here that I have been 'meaning to read'... they 'll sure to be good 13:40:50 "suggested model for prebiotic evolution: The use of chaos" 13:41:03 <_dan> ive been getting quite a lot of pleasure out of going through my papers libraries and picking out the old papers in there (2000-2002) and re-reading them in the cold light of my new found knowledge 13:41:13 "What is a desirable statistical energy function for proteins and how can it be obtained?" 13:41:34 "Improved protein structure selection using decoy-dependent discriminatory funcitons" 13:41:37 feh! boring! 13:42:16 Hrm, leaving the terminal ceases my existence? 13:42:26 Reviews count, I think. 13:42:27 yes 13:42:34 the use of chaos, heh 13:42:58 Meh, those sound relatively interesting. 13:43:01 "conservation and prediction of solvent accessibility in protein families" <- that one is nice... 13:43:07 oh.. I got one... 13:44:24 PairsDB atlas of protein sequence space. 13:44:26 and 13:44:35 The global trace graph, a novel paradigm for searching protein sequence databases. 13:44:38 I like them 13:44:45 http://www.ncbi.nlm.nih.gov/pubmed/17986464 13:44:58 http://www.ncbi.nlm.nih.gov/pubmed/17823134 13:45:08 Liisa Holm is great 13:45:39 Heh, expecting to read a paper in 10 minutes or less isn't the best of strategies. /me reads quickly 13:46:54 the 'global trace graph' paper, while algorithmically elegant is not well written 13:47:23 also... (since you asked) ... a paper I enjoyed reading was "Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures" 13:47:41 the fact that they sequenced 12 genomes is impressive alone, but the data they found is amazing 13:48:21 oh oh ... Wans paper on 'mirror trees' is a great read! Seriously, Wan is one of the smartest people I have ever met 13:49:12 http://www.ncbi.nlm.nih.gov/pubmed/14764552 13:49:58 Its "Wan Kue Kim", I always get confused by the order of characters in korean names 13:50:43 his name in english should be 'Wan Kue', but we called him wan because 'Wan Kue' isn't the best name in england 13:51:01 hehe 13:52:00 ;-) 13:52:16 We should make a channel page somewhere... everybodies top 10 Bioinf papers... 13:52:25 well... I goes home now. 13:52:45 kanzure: tell wan you know his evil twin (dan). 13:52:53 we both worked with Jong 13:53:00 Is that so? 13:53:11 yup, that last paper is the three of us 13:53:33 so, pronunciation? 13:53:40 Wan as in wireless area network? 13:53:59 wan ... as in ... er ... yeah... the way i say it anyway... 13:54:18 ur american right? 13:54:46 its basically wan as in one of our british wankers... but most americans don't know what that is... (he is far from it btw... 13:54:49 * faceface blushes 13:55:14 he won't mind anyway... if you see him that is... anyway... I goes now 13:55:17 *** faceface has quit ("Bye, and thanks... probably.") 14:30:10 *** toru has quit ("Ex-Chat") 17:41:43 *** highvoltz has quit () 17:50:41 Could anybody give me a hand? I need to combine two csv files (but they are way to big for excel / open office). I have to put one csv file with two columns in front of another csv files with 7066 columns. Anybody got any idea 18:07:20 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 18:34:31 *** jeanne (n=ada@adsl-84-227-68-31.adslplus.ch) has joined #bioinformatics 18:34:36 hi 18:34:53 does anyone know restriction enzymes which doesnt cut the Escherichia coli genome ? 18:35:34 jeanne: Just go get a table of restriction enzymes, see what they cut, then make sure that's not in the ecoli genome. 18:36:53 is there an efficient way to do that ? I am biologist... 18:37:08 I'd argue that it is efficient. Hold on. 18:37:23 Here's your list. 18:37:23 http://www.thelabrat.com/restriction/index.shtml 18:37:42 http://www.genome.wisc.edu/sequencing.htm 18:37:45 There's your ecoli genomes. 18:38:29 ty for the lists 18:38:44 http://www.genome.wisc.edu/sequencing.htm 18:42:20 Fse I cuts 4 times 18:44:04 is there noone who could check that with an algorithm here ? 18:44:11 not this handy to do it by hand.. 18:44:32 e.g. matlab bioinfomatics toolbox or so ? 18:46:44 jeanne: it would be wise to create an application that scans a sequence (of a E. Coli genome) in comparison with your restriction enzyme. 18:47:00 jeanne: Do you need this one a short notice? 18:47:34 I have here the sequence: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?WebEnv=0u-aarheDB6YDyT6sZJ73JYOquVDSYiH0r7hC97B_zoRzmcag7GrmDfqJ1Ka3TOLViCkEwicnSUSjfg@2563578984ECB4B0_0103SID&db=nucleotide&qty=1&c_start=1&list_uids=NC_000913&uids=&dopt=fasta&dispmax=5&sendto=&fmt_mask=295416&truncate=294912&less_feat=504&from=begin&to=end&extrafeatpresent=1 18:47:48 and there are a lot of restriction enzymes 18:48:00 but I need only those which do not cut the e coli genome 18:48:16 I have made an application like that little over a year ago, I don't think I have it around any more. But if you not need it asap I could recreate such a thing for you during the summer. 18:48:30 shouldn't this take just 20 minutes 18:48:35 load up the genome, then search 18:48:56 I need it faster 18:49:12 until tomorrow evening 18:49:46 load up to where ? 18:49:47 jeanne: Yes but it depends. a restriction enzyme might also cut from 3' to 5' but also from 5' to 3' (I have the docs on this lying about somewhere to) I can't recollect entirely but it is more then just scanning the sequence as I can remember. 18:50:50 thats true a restriction enzyme which recognizes a restriction sequences can cut it independent of it is on the 3-5 strand or 5-3 strand 18:53:39 There should be a schema of restriction enzymes who do cut up the e. coli genome. Then pick one that isn't on the list. That would be the quickest method. You can check this by opening the genome sequence in a text editor and do a search with the restriction enzyme sequence (also the palindrome for the '5 to '3 effect) 18:54:37 If it doesn't match anywhere you have a winner. But i would investigate a bit further after that. (Is this for a real experiment? I know this stuff doesn't come cheap) 18:56:16 yes it is for a real experiment 18:57:07 Then I would seriously reconsider the time scale. If you only have a day and a half do figure such things out it won't do the results much good. 18:57:46 Don't get me wrong I know how these kind of things go. But that is my genuine advice. 18:58:04 yes 18:58:13 I see your point 18:59:20 do you know matlab ? 18:59:39 Nope sorry. I am more of a GNU R type myself 19:00:13 octave is the gnu matlab replacement 19:03:22 ok 19:29:46 jeanne: load it up into memory 19:29:49 into a variable 19:30:26 I try that at the moment... 19:30:35 unfortunately I dont know how to read in a file in matlab 19:30:43 bah, just do it with perl 19:30:45 http://bioperl.org/ 19:31:02 ok 19:33:20 open(INFILE, "mousegenome_file.txt"); 19:33:21 $file = : 19:33:21 close(INFILE); 19:33:21 if($file =~ s/the restriction enzyme sequence here/) { print "ERROR! Please try a different restriction enzyme."; } 19:33:27 Something like that. 19:33:45 http://perl.org/ 19:33:46 or see #perl 19:34:40 hehe mouse.. 19:35:06 99% cut the genome 19:35:10 i assume 19:44:15 ? 19:45:55 Well, there's 4 possibilities per nt, so for a length 4 strand that's 4^4 aka 256 possibilities, or if the length is 8 then that's 4^8 or 65536, and at 4^16 (length=16), that's 4294967293 or something. 19:46:12 The mouse genome is only 2.7 billion bp in size. So around length = 16 to length = 24, you start approaching those numbers. 20:16:16 computed now all enzymes which cut e coli and the responding sites 20:16:27 but I need the ones which dont cut 20:16:48 have somehow to subtract the whole list from cutting ones 20:18:15 *** kanzure has quit ("Leaving.") 20:30:37 *** jeanne has quit ("Ex-Chat") 21:03:15 *** ybit has quit (Remote closed the connection) 21:12:34 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 21:41:59 *** berry_nl has quit (Connection timed out) 21:44:37 *** berry_nl (n=berry@vpn-out.hsleiden.nl) has joined #bioinformatics 22:18:17 *** berry_nl has quit (Read error: 110 (Connection timed out)) 22:18:53 *** ybit has quit (Remote closed the connection) 22:42:38 *** synthase (n=synthase@69.254.170.145) has joined #bioinformatics 23:11:02 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 23:25:20 *** synthase has quit (Connection timed out) 23:25:29 *** synthase (n=synthase@69.254.170.145) has joined #bioinformatics