this is a recording of a biomoo session held on 12/12/96 on section 4 of the course material

ClareS turns the ClareS_recorder on.

ClareS says "I have now started recording this session. The transcript (and yesterday's) can be read in this room, and will be available on the mailing list archives"

(Jim Pitts has connected.)

ClareS says "it would help if you all had access to a web browser pointing to section 4 of the course material"

ClareS says "but there should also be time for some more general discussion of the course so far"

ClareS says "Do any of you have any specific questions about section 4, which one of us could help you with?"

ClareS [to henryb] I have a practical question for you -


ClareS [to henryb] I have been looking through your web exercises on DNA structure etc., and it's not finding the PDB files

Henryb [to ClareS] Yes, sorry I was at Daresbury?

Cockle finds his way in.

ClareS [to henryb] the PDB files in the directory /Departments/BioSci/PPS/PDBfiles/ do not appear to be accessible

Henryb [to ClareS] I have lots of them now and I don't know which one you are referring to?

ClareS [to henryb] an example is 122d.pdb

Henryb [to ClareS] which file were you looking at?

Jim Pitts says "If you go to and click DNA molecule it bounces!"

Jim Pitts says "Hi there"

Benito finds his/her way in.

Cockle says "hello"

Jim Pitts waves

ClareS says "hello to newcomers, we're discussing section 4 of the course material"

Benito says "hello"

ClareS says "While Henry answers the phone IRL, how many of you are using the Chime plugin?"

ClareS says "Chime is really useful, but unfortunately is only available for the Windows platform so far - if you are using Mac or Unix you won't be able to take advantage of it yet"

Hagar says "to Henryb The directory pointed to should be PdbFiles, not PDBfiles"

(Camillo has disconnected.)

ClareS says "Is anyone having serious problems with the connection?"

(Camillo has connected.)

ClareS says "there seems to be a problem with lag (worse than usual)"

ClareS says "How has everyone found this section of the course material?"

Henryb says "Since there do not appear to be any questions then maybe I should pose you all one. Now that we have sequenced a few genomes (Haemophilus influenza, M leprae, yeast and E coli) is there anything left to discover now we know all the proteins

that make up life? "

ClareS says "Are there any problems with it - or are you finding it easy enough, or too easy?"

ClareS [to henryb] There are still very many unknown mammalian genes

Henryb says "Clare mentioned that there was a problem wiht accessing a pdb file from one of my pages. I thought that this was a problem with a missing file. However, this even stranger than I originally thought. The file is there so the fault lies elsew

here. I will have to look into this one and sort it."

Hagar says "to Henryb When we have all the bits of the jigsaw - we still have to put them together"

ClareS says "and, of course, there's still (I think?) about a 30% chance that any new protein will have a new fold"

Jim Pitts [to ndnd] eeee

Henryb [to Hagar] Yes, that will be the interesting job. Running a DNA sequencer is not much fun but making sense fo the sequence is the challenging job. But you can't do the interesting job until you have finished the mind numbing one.

ClareS agrees

Jim Pitts [to ClareS] How is this

Jim Pitts [to ClareS] It is a bit slow responding

ClareS says "Previously (decades ago) the very fact of sequencing a piece of DNA was worth a good paper - now it's routine"

ClareS thinks that the really exciting science is in relating sequence to structure to function...

Hagar says "to Henryb the file access problem is a case one, it should be PdbFiles, not PDBfiles"

Henryb says "so what will happen once we have identifed all the genes in the human genome. What will be the next stage?"

Doohun [guest] agrees to ClareS

ClareS [to Hagar] thanks for pointing that out

ClareS [to henryb] the sequence is (now) the easy part! relating that to function is much harder

ClareS . o O ( and much more fun )

(Gail0 [guest] has disconnected.)

Jim Pitts says "How do you know the sequences are right, should you sequence at least three different members of the species?"

Henryb says "assuming there are no sequence errors. I've recently spent a lot of time tidying up the two ends of a DNA seqeunce in the databank."

Henryb [to Jim Pitts] Pitts Sorry, you beat me to it!!!

ClareS says "the next section of the course material will be an introduction to bioinformatics (sequence analysis)"

Henryb says "A lot of sequences come straight off sequencers into the database and are untouched by human hand. The computer remoc=ves obvious rubbish and submits the sequence. There wiil be errors. Maybe I should come to the bioinformatics course."

ClareS says "and you will find out much more about what can be learned from DNA and protein sequences"

Jim Pitts says "One advantage of old fasioned biochemistry was that you extracted your protein from lots of material from several animals, so the odd nutant was diluted within the whole amount of proteins, more or less"

ClareS smiles at Henry

ClareS says "so, there are problems with making everything automatic - it's just too easy"

Jim Pitts says "fashioned mutant that is"

ClareS says "this was pointed out at the Bioinfo conference I've just attended - there are many more errors in sequencing now, because it's much less skilled"

Hagar says "Unfortunately the functionality of some protein familes relies upon the allelic point mutations of otherwise identical sequences"

ClareS [to henryb] do you agree?

Henryb [to Jim Pitts] Yes. That's the problem with sequencing the human genome. Do we know we have sequenced a 'wild type' human.

ClareS . o O ( I always wondered just *whose* genome would be sequenced ;) )

ClareS . o O ( *every* "human genome" is different... )

Henryb [to ClareS] Yes. The database is now filled with sequences obtained by robots (quite literally).

Jim Pitts says "I heard a rumour the Ronald Regan was going to be used, I would have been happy if they needed ALL his DNA for the experiment "

Henryb says "I thonk that "

ClareS grins

Henryb says "I think that the current sequencing is just a low resolution map. It will tell you where there MAY be something of interest. Then you have to look in more detail and resequence."

Doohun [guest] smiles

Henryb says "Sorry for the delay to that message, I'd forgotten what I was thonking"

ClareS [to henryb] can you guess what % of the human genome will turn out to be "junk" DNA?

MD finds his way in.

MD says "Hi Everybody!"

MD says "Sorry, I'm a little bit late!"

ClareS [to MD] Hi! We're discussing the human genome program

ClareS [to MD] A lot of people are lagging - the connections seem to be slow today

Henryb [to ClareS] Very diffficult to estimate when the deinition of 'junk' is vague. People talk about 10-30% of the human genome being coding.

ClareS says "I *think* (it's not my main subject area) some bacterial genomes have much higher percentages of coding sequence"

Henryb says "Yes, bugs use about 90-95% of their DNA."

ClareS hadn't realised it was *that* high

Hagar says "to ClareS Yes and so probably to some vertebrates, such as the puffer fish"

MD says " I have no problems, I opened a www and telnet session without any problems. Yesterday it was more complicated."

ClareS [to MD] there are no real problems other than speed (or lack of)

MD says " I think it is still a time-zone problem too. Yesterday I locked 1h to early. The best thing is to make a little (local) time table :-)"

ClareS [to MD] you can check the time here (in Israel), in GMT and in your "home" timezone by typing the word "time" from within BioMOO

MD says " But I will not restart this discussion. But I tire to reconfigure our timed."

ClareS [to MD] it's going to be impossible to find a time to suit everyone, each time we have a meeting

MD says " But not everybody knows the code of this 3 letters: GMT Greenwhich mean Time (?!)"

ClareS says "there is a Greenwich website, but I have forgotten the URL"

ClareS says "before we close the "formal" part of the meeting, tho', are there any more questions or comments for Henry"

ClareS says "or is there anything else about the course itself you'd like to discuss?"

Doohun [guest] says "it is"

ClareS [to Doohun] thanks!

MD says " Ok. Let us discuss about the human genom project: who"

Hagar says "Goodbye everyone"

(Hagar has disconnected.)

Henryb says "If there are no more questions for me I will try and sort out the web page."

ClareS [to henryb] thanks for coming, and sorry about the connection problems

Henryb [to ClareS] Nice to see you, and everybody else. Connections are always variable c'est la vie. Happy Christmas to everybody.

ClareS [to henryb] Happy Christmas to you, too!

Henryb says "Bye all"

ClareS waves

(Henryb has disconnected.)

Doohun [guest] says "bye henryb"

ClareS turns the ClareS_recorder off.