MUD transcript: 22-02-00
Introduction to Bioinformatics
Course room(s): PPS
23:01:35 ClareS connects.
LarryT PPS Telnet 7m 14s 2m 53s
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23:01:41 ClareS says "Hi"
23:02:00 ClareS says "I'd prefer to wait around a bit to see who else arrives... if that's OK"
23:02:28 LarryT says "Hello from "the colonies" (g) That's OK I am practicing my lurking skills"
23:02:39 VijayK connects.
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23:04:07 VijayK says "Hello and good evening. I have not yet heard fro you tonight. It is 23.03 GMT"
23:05:32 VijayK says "I geuss Larry will be with us soon"
23:06:06 LarryT says "I am lurking ...we are waiting a bit for more to arrive"
23:06:41 VijayK says "Thanks !Atlaeast you are lurking"
23:07:09 ClareS says "Hi"
23:07:27 ClareS says "welcome.. we can wait a couple of minutes I think"
23:07:49 VijayK says "Care can we start something with something we discussed about last time?"
23:07:53 ClareS says "there is at least one other trying to join us, but she lost her password in a computer crash"
23:09:26 VijayK says "I checked on the homolgy bit. I thnk we were referring to different things. What I think is that you were referriing to structure homology and I was talking about sequence homology. Is that right?"
23:09:53 ClareS says "OK -- let's start now"
23:10:35 ClareS says (to VijayK) "I don't have the transcript up yet; can you remind me what you were talking about, please?"
23:10:48 ClareS says "(this will be useful for the transcript, too)"
23:13:23 ClareS looks round expectantly
23:13:49 ClareS says "structural homology is rather an odd term"
23:14:26 ClareS says "if two sequences are homologous, it simply means that they are evolutionarily related"
23:15:58 ClareS says "(sorry, I lost the connection)"
23:17:38 VijayK says "Well you asked a question about homology and said that homology relates to the folds. But I pointed out according to the URL I cited that folds relate to anologous structures. I loooked further in the section Implications of primary structure which also sid that homologous protiens are related by similar sequences. But I want to know if protiens are similar in thier 3D strucutre, that would show a strucutural homology."
23:17:45 ClareS has lost the connection twice in the last 5 minutes: are you still there?
23:18:31 ClareS says "as I was saying, you can't distinguish between "sequence" and "structural" homology"
23:18:44 ClareS says "the way you can with "similarity""
23:19:02 ClareS says "if two sequences are homologous, they will have similar sequences and a similar fold"
23:19:23 ClareS says "but the degree of similarity will differ"
23:19:52 VijayK says " Iam trying to get it. I will work harder. Thank you"
23:20:05 ClareS says "and there are proteins that have similar folds although they are not evolutionarily related"
23:20:30 ClareS says "these sequences are called analogues, and they got that way because of a process called convergent evolution"
23:20:59 ClareS says "the TIM barrels are examples of this"
23:21:09 ClareS says (to VijayK) "does that make any more sense?"
23:21:51 VijayK says "TIM barrels was mentionerd last MUD. I will look uo again"
23:22:36 ClareS says "don't worry too much about this, you will study TIM barrels later in the course"
23:22:39 VijayK says "But convergent evolution is new. Menas More work."
23:23:08 ClareS says "convergent evolution is quite a simple concept"
23:23:26 VijayK says "Why is Larery not saying anything"
23:24:03 ClareS says "all it means is that two sequences *just happened* to evolve into similar structures because that pattern is energetically favourable and good for a particular task"
23:24:06 VijayK says "Sorry for the typo. I mean Larry"
23:24:15 LarryT says (to Say) "I like to listen more than speak and I type poorly!"
23:25:14 ClareS says (to LarryT) "that's OK -- which is why the more people that turn up the better, within reason"
23:25:33 VijayK says "Clare are we talking a bit about finger printing tonight"
23:25:48 ClareS says (to VijayK) "do you understand what I said about convergent evolution just now?"
23:26:14 ClareS says (to VijayK) "I'm not clear what you mean by fingerprinting"
23:26:37 VijayK says "Yes almost. But I have to read the transcript and get a bit more idea about it later"
23:27:07 VijayK says " the section about sequence analysis"
23:28:13 LesleyM connects.
LarryT PPS Telnet 33m 52s 3m 58s
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VijayK PPS HTTP 25m 34s 1m 6s
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23:28:45 ClareS says "you mean, in the BioActivity tutorial -- fingerprint scans?"
23:28:52 ClareS says (to LesleyM) "welcome!"
23:29:14 LesleyM says "hello sorry I was delayed"
23:30:05 ClareS says (to LesleyM) "don't worry about it"
23:30:20 ClareS says (to LesleyM) "we have been talking about homology and convergent evolution"
23:30:26 VijayK says "I am referring to the information in the prints fingerprint data base. There is a bit for which I need some more explanation"
23:30:41 LesleyM says "I am just getting into the swing of the bioinformatics - pity it's time to move on."
23:31:05 ClareS says (to VijayK) "I thought you might mean that -- what exactly are you puzzled about?"
23:31:32 ClareS says (to LesleyM) "you could always do a bioinformatics related project if you like: there are always a few on the list"
23:32:50 VijayK says " The list - ptm etc. You see there are two columns after the compound column they say p and give a number"
23:33:49 ClareS says "I will have to look this database up on the web as I can't remember the exact format"
23:33:51 LesleyM says "how useful, generally, is it to have the swissprot graphics program"
23:33:57 VijayK says "E.g. GLABLOOD p 3 ..."
23:34:41 VijayK says "what are P and the number (3) for?"
23:35:14 ClareS says (to LesleyM) "you mean Swiss3DModel: that is a graphics program that is more complex and more useful than Rasmol"
23:35:27 ClareS says "as it'll allow you to do some simple molecular modelling"
23:35:44 ClareS says "but it is rather harder to install and use, and doesn't run on quite as many types of computer"
23:36:24 LesleyM says "so you would say it's worth having installed?"
23:37:20 ClareS says (to LesleyM) "yes, but you can manage without it"
23:37:44 ClareS says "the fingerprint GLABLOOD is a complex fingerprint that consists of 3 motifs"
23:38:14 LarryT says "the Windows version of Swiss Model is worth the FREE price of download ...there are a lot of packages (plugins for it), but it was relatively straightforward"
23:38:14 VijayK says "Thank you Clare"
23:38:17 ClareS says "that is, each of 3 separate sequence segments need to match if a sequence is to match the motif fully"
23:38:47 VijayK says "It is clear now"
23:39:32 ClareS says "if you go to http://www.bioinf.man.ac.uk/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=/Full&fun_a=Code&qst_a=GLABLOOD you will see the full entry for that fingerprint"
23:39:48 ClareS is not at all sure if such a complex URL is clickable from her
23:40:00 VijayK says "But some of the compounds have P in the second column and others don't"
23:40:00 ClareS meant "from here", of course
23:40:50 VijayK says "Right"
23:41:13 LesleyM says "I have a very simple question: aat the very beginning of the tutorial, in translation.."
23:41:55 ClareS says (to LesleyM) "yes, go on..."
23:42:27 LesleyM says "how does the reverse translation work..I can follow the forward one OK"
23:43:59 ClareS can't remember a reverse translation in that tutorial
23:44:17 ClareS says "I assume you mean a translation from protein back to DNA?"
23:44:53 VijayK says "That comes from the exercise Nucleac Acid Translator"
23:46:03 LesleyM says "no - the translation gives six amino acid sequences, dependending which nucleotide it starts at.."
23:47:04 LesleyM says "the sequence is obviously different if it starts at nuc. 1 rather than 2.."
23:47:12 ClareS says "you can't get from a single protein sequence back to the DNA, because of the redundancy in the genetic code"
23:47:42 ClareS says "you could if you wish get back from the 3 frame translation, but it's not a very useful calculation"
23:48:02 LesleyM says "the tranlations are quite obvious to me for the forward tranlations but not for those labelled reverse"
23:48:24 VijayK says "Do you say that it was ok for the sake of exercise?"
23:48:24 ClareS says "oh, I see, sorry.. I misunderstood you"
23:48:43 ClareS says "the translations labelled reverse are those on the reverse strand"
23:49:18 ClareS says "the reverse complement of the sequence that you put in -- as the coding sequence could just as well be on the other strand of the DNA"
23:49:24 ClareS says "is that clear?"
23:49:38 LesleyM says "why does it give those?"
23:49:52 ClareS says "say you had a (very short) sequence CGAT"
23:50:16 LesleyM says "OK"
23:50:16 ClareS says "the reverse complement of that sequence is ATCG, can you see why?"
23:50:28 LesleyM says "yes"
23:50:48 VijayK says "yes I think if we match TG with AC on the reverse strand"
23:51:16 ClareS says "you can't assume that the DNA sequence you have been given is on the strand that codes for the gene"
23:51:42 ClareS says "to reverse complement you start at the end of the sequence and replace each base with its complementary one"
23:52:18 VijayK says "Yes I meant that"
23:53:13 LesleyM says "OK I can follow it now - I was literally reversing the sequences and trying to translate them - to no avail!"
23:54:13 ClareS says "and I misunderstood your use of the phrase reverse translation, sorry"
23:55:05 ClareS says "I would like to finish this session soon <yawn> ; are there any more questions or comments?"
23:55:43 LesleyM says "that may be a point to clarify in the tutorial - perhaps add in "complementary" somewhere"
23:56:29 ClareS says "we didn't write this tutorial, but I'll try to remember to mention it to Terri Attwood (who did)"
23:57:00 LesleyM says "thanks for your help -over and out from me."
23:59:20 LesleyM disconnects.
LarryT PPS Telnet 1h 4m 7s
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23:59:57 ClareS looks round expectantly
00:00:07 ClareS yawns
00:00:57 ClareS says (to LarryT) "I think that "fungers" is an excellent word!"
00:01:17 ClareS grins
00:02:16 VijayK disconnects.
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00:04:13 LarryT says "well.t's late in the motherland, so the colonies will depart"
00:04:25 LarryT disconnects.