BioMoo Transcript from 28-1-98

GeorgF turns GeorgF's recorder on.

GeorgF turns GeorgF's recorder off.

GeorgF turns GeorgF's recorder on.

ClareS finds her way in.

ClareS drops the jan28tape.

ClareS points the ClareS_recorder at the jan28tape.

BMD finds his way in.

BMD says "G'morning"

ClareS says "Hello"

ClareS says "glad you could make it.., sorry for the short notice"

BMD says "I'm glad you could make it too.....I was told that there was a chance you would not."

ClareS will wait a few minutes

ClareS says "I am currently in Poland IRL.. the connection is *very* dodgy"

ClareS says "that is why I "invited" Georg here to take charge"

GeorgF waves.

GeorgF is lagging

BMD [to GeorgF] Good to 'see' you Georg!

JudyH finds his/her way in.

ClareS says "Hi"

ClareS says "glad you could make it..."

ClareS says "I don't think morning meetings will be very popular.. but several of you wanted one, so we're trying the experiment"

ClareS [to JudyH] is this time best for you, or is the afternoon equally good?

JudyH says "Afternoons are better, I can listen in this morning on & off if I miss my coffee"

JudyH says "As there doesn@t seem to be many here I,ll ask a general question; I have been wondering how much of the information in the links we need to retain for the exam. Are there any old exam papers to look at? I know its a long way off..but it"

JudyH says "could make it easier to know when to stop!"

ClareS says "I agree - morning meetings will probably be discontinued"

Jim Pitts finds his way in.

ClareS says "it would be worth having a general chat about the course (& exam)"

ClareS says "Hi Jim"

Jim Pitts says "Hi Clare"

Jim Pitts says "Had problems getting in!"

Jim Pitts says "Sorry I am so late"

ClareS [to Jim Pitts] as there are so few of us here (& I'm lagging horribly) we're just having a general chat about the course

ClareS [to JudyH] there *are* old exam papers - but it probably wouldn't be a good idea for you to look at them yet

BMD [to ClareS] Why?

JudyH says "I thought the speed might be better in the morning but it isn't!"

ClareS [to JudyH] we have only covered about half of the course material - you might get discouraged

JudyH says "yes I probably would!"

BMD says "I find peering at the exam paper rather...well...motivating."

ClareS says "we will be having the "self-assessment" section of the course soon"

JudyH says "will the self assessment be similar in difficlty to the exam?"

ClareS says "the self assessment will have two components"

ClareS says "firstly multi-choice quizzes"

ClareS says ".. and then, some short answer questions - we will send these by email"

ClareS says "the self assessment will cover the same material as the exam, so will be the"

ClareS says "same standard - but the questions will be much shorter"

ClareS says "either multi-choice or short answer instead of full length essays"

JudyH says "Thanks Clare that Clarifies it"

ClareS says "we can handle the short answer questions one of two ways..."

ClareS says "either we just send the questions, and then send some model answers by email a few weeks later..."

NickyM finds her way in.

ClareS says ".. or we ask you to return your answers and mark them..."

ClareS says "which would you prefer"

ClareS [to NickyM] Hi - glad you could make it

ClareS [to NickyM] as there are few of us here we are having a general chat about the exam and self-assessment

NickyM says "sorry I'm LATE"

BMD says "I would have a question regarding the multitude of sequence databases available on the net. I am sure there's quite an overlap between them. Does one evetually stick to one source?"

ClareS [to NickyM] don't worry about it...

ClareS thinks we will go back to afternoon meetings

NickyM says "is this the exam at the end of the year?"

ClareS [to NickyM] yes... you don't really need to worry about this yet

JudyH says "I think I would prefer at least a couple of answers to be marked, so to get an idea of the standard "

DavidM finds his way in.

ClareS [to BMD] re

Jim Pitts says "Hi"

BMD [to ClareS] Annotated?

Tracy finds her way in.

ClareS [to BMD] in terms of extra information, not just the sequence

BMD [to ClareS] Does one protein have a UNIQUE identifier across all databases or does each database use its own?

ClareS [to BMD] each database iuses its own, but they are all cross-referenced

BMD [to ClareS] Which are the most authoratitive? {without sparking much controversy ;-)}

ClareS [to BMD] are you principally thinking of protein, or NA sequence databases?


BMD [to ClareS] Should there be a difference?

ClareS says "If you are thinking of protein databases, then there is no controversy at all. the best annotated sequence database is with no doubt SwissProt"

BMD  hmms.

ClareS says "protein databases record the AA sequences of proteins, NA databases... the base sequences of genes"

BMD [to ClareS] And what about NA sequence databases?

ClareS says "so the info held in a DNA seq. database will include, often, non-coding regions"

ClareS says "and will also give e.g. info on codon usage"

ClareS says "protein sequence DBs contain other information, such as, for instance, function and expression"

ClareS says "and links to e.g. a 3D structure if one is known"

BMD [to ClareS] I see.

ClareS says "you might find it helpful to turn to the ExPASy home page and look at a "random" SwissProt entry"

ClareS says "the URL is then follow links to SwissProt"

BMD [to ClareS] What are the pre-requisites to include a 'new' NA sequence to a database....what info must be included with it?

ClareS is not an expert on NA sequencing

ClareS says "but I know that a lot of the annotation is still done by the database curators"

ClareS says "If you select a random swissprot entry (NOT TREMBL) you wil see some of the annotation and cross-links - this is why SwissProt is so widely used"

BMD [to ClareS] If one were to try and establish the evolutionary distance between two similar proteins in different organisms, does one align the protein sequence or the NA sequence...or both?

Tracy says "'can you recommend a good website which gives an overview of databases concerned with gene sequences'"

ClareS says "Both - you should get similar answers, of course, but there is more info in the NA seq. alignment"

ClareS says "as you can see the codon usage"

GeorgF [to BMD] >does one align the protein sequence or the NA sequence< There was a long discussion last week about this, in bionet.molbio.evolution, Re

ClareS says "so you can see *exactly* how many base changes have taken place (the minimum, of course"

ClareS [to GeorgF] very useful point... brings me to the usefulness (within reason) of Usenet News ;)

ClareS says "I hope you're all using the Biomet newsgroups"

ClareS . o O ( Biomet = Bionet, I can't type )

ClareS [to GeorgF] was there a consensus answer? this is more your field than mine

GeorgF says "also, Jotun Hein has written a program (and papers) on the simulanous alignment of both the protein and the nucleotide sequence"

ClareS [to tracy] there are 3 linked universal, comprehensive nucleic acid databases - GenBank, EMBL and DDBJ

GeorgF hasn't read the thread yet, just saved it No time -/

BMD says "Alignments are so 'confusing'...there always seems to be more than one 'optimal' match...and it seems that the strength of the 'optimality' changes according to the weights allotted to the different types of mutation."

Jim Pitts finds his way out.

ClareS [to GeorgF] do you have the reference to hantracy, the real difference between those databases.. is merely location

Jim Pitts finds his way in.

ClareS [to tracy] the data held in them is the same (apart from really recently submitted sequences) but EMBL is in Europe, GenBank in the US and DDBJ in Japan

ClareS has been lagging and sending confusing messages

ClareS apologises (

ClareS [to GeorgF] *Do* you have that reference?

ClareS says "each of those databases is located at a Web site which holds a lot more information about NA sequences than just the databases"

ClareS says "for example, for EMBL and a lot of other stuff see the EBI site:"

ClareS says ""

Tracy says "'thanks I'll look further'"

BMD [to GeorgF] What makes one alignment technique more reliable than another?

ClareS [to BMD] are you talking about simple pairwise alignments, multiple alignment or scanning a database for homologous sequences?

BMD says "I am talking about the underlying principles...."

BMD says "in the consideration of probability of mutation"

BMD says "as outlined in the Dayhoff matrix."

ClareS says "the technique you use *will* vary... for aligning 2 sequences you will be able to use a more complex algorithm than if you are scanning a database of many thousands"

BMD says "That seems to be the 'bottom-line' for any sequence alignment."

NickyM says "in answer to an earlier question - I'm afraid I don't use Bionet, Should I?"

BMD [to ClareS] I understand.

ClareS says "You can't do much better for database scanning than just intelligent use of Blast and/or FastA. IMHO, anyway ;)"

ClareS [to NickyM] Bionet is very useful, but like all internet tools, it's possible to spend much too much time on it

GeorgF can't find the reference to Jotun Hein's paper, sorry..

GeorgF says "Anyway, Hein's program doesn't seem popular, probably"

ClareS says "there isn' much time in the PPS course to do more than just touch on this complex area"

GeorgF says "because it uses a lot of time, but frankly I don't know."

ClareS says "if you want to explore the area more thoroughly.. you can start by looking at Georg's Biocomputing course web pages"

ClareS [to GeorgF] what is the URL? I can't remember off hand

GeorgF says "h"

GeorgF says ""

BMD says "I cannot understand the difference between BLAST, FASTA, scanPROSITE, ProfileScan at ISREC and PFam at Sanger's. They seem to be doing the same thing really. Is that so?"

Tracy says "'Don't proteins have various regions i.e. regions to bind to other proteins/DNA, catalytic regions? Once you have homology this doesn't necessarily confirm function, does information regarding mutants get put on a database?'"

GeorgF says "For Multiple Alignment, Clustal is the most popular, Gotoh's method seems to be the most accurate, but few ppl use it b/c the code isn't easily accessible, and DCA/MSA is also worth a look. SEE

MulAli/welcome.html for pointers"

ClareS [to BMD] Blast and FastA do very similar things

ClareS says "ScanPROSITE and the other things you mentioned are different - they look for *patterns* in protein sequences"

ClareS says "which are likely to give you a guide to the function of a sequence"

ClareS says "i.e do they contain calcium-binding regions, nucleotide-binding regions, characteristic sequences for e.g. serine proteases, etc"

BMD [to ClareS] You mean, different classes of patterns => different search engines?

ClareS says "If *homology* (an evolutionarly relationship, remember) can be proved by alignment this is a *very good* guide to function"

ClareS says "but many proteins with the same function are not strictly homologous"

ClareS says "this is one occasion where sequence patterns are very useful"

ClareS says "Patterns in protein sequences have been classified in several different ways"

ClareS says "the three best known are,,probably, Prosite, Prints and Blocks"

ClareS says "each has a slightly different set of patterns"

ClareS says "one important difference is that Prosite includes very short patterns such as glycosylation and myristylation sites"

BMD says "So Prosite, Prints and Blocks are useful when one has a novel sequence of NA/AAs and wants to check its functional association with other known proteins."

ClareS says "bmd, not quite... Prosite etc. only work with protein sequences. If you have a NA sequence you would have to translate it into protein (and check that it represented an ORF, at least) first"

BMD says "I see."

ClareS [to BMD] is that OK?

BMD [to ClareS] Yes, thank you.

ClareS says "I have just looked up the URL Georg gave us re: multiple sequence alignment: it certainly represents a very comprehensive and useful list of resources"

ClareS . o O ( yes it *did* take Netscape that long to load the page )

ClareS says "I am looking forward to trying out e.g. ClustalW alignments in colour"

ClareS says "This is a very interesting discussion, but I think we should close the "formal" (i.e. recorded) part of the session soon. Does anyone still have any important questions?"

NickyM says "For the sequences in section 5 - with all these 'matches' from the different databases, is there a way to judge the 'correct' one ie the first one. Some times the only difference is the source (human, mouse etc) and we don't know this or am

I missing something?"

Jim Pitts says "I would like to ask if the session time caused many or any problems to you?"

Jim Pitts says "As the numbers seem a bit low."

ClareS says "I think that the fact that there have been so few of us here indicates that most people would prefer afternoons (Europe time): do you agree?"

JudyH says "N0, I think that was a uaseful session; I have enjoyed doing this section, but now have more of an overview on how you would use the searches"

Tracy says "'yes, mornings are difficult, sorry I was late'"

JudyH says "yes afternoons are best for me"

ClareS [to JudyH] thanks, glad it was a useful session

BMD [to ClareS] Early GMT afternoons on Thursdays are a bit of a problem for me, but that's just about it.

ClareS says "that seems to be a couple more votes for afternoons - and we'll try to make sure they're not too early"

ClareS [to BMD] what time is too early for you?

BMD says "I am unavailable on Thursdays from GMT 1300 - 1400"

ClareS says "I can't recall setting any meetings at that time (lunchtime in the UK ;)"

BMD says "Righto"

ClareS [to NickyM] I'd like to try the exercises myself again before getting back to you - once I'm back in the UK (late this week) & have a "normal" line back.

NickyM says "Thank you Hope you're somewhere warm and sunny!"

ClareS [to NickyM] is that OK/

ClareS [to NickyM] actually it's snowing ;)

Tracy says "'must go, thanks for your help'"

JudyH says "me too, bye"

(JudyH has disconnected.)

(Tracy has disconnected.)

GeorgF turns GeorgF's recorder off.