BioMOO Transcript for 26-1-99

ClareS turns the ClareS_recorder on.

ClareS says "Welcome to the first of our two Bioinformatics meetings..."

ClareS says "the lines appear to be slow today, and there are few people here, but I hope yyou find it useful"

ClareS says "I would first like to introduce Georg Fuellen (GeorgF) who runs an Internet based course in bioinformatics from Bielefeld, in Germany"
AndyS finds his/her way in.

ClareS [to AndyS] Hi

ClareS [to AndyS] we've only just started.. I have just been introducing our guest speaker

AndyS says "Hi sorry I'm late"

ClareS says "Do any of you have any particular questions?" GeorgF smiles. "guest speaker" is a little over-stated... I'm currently writing my thesis, so I can answer questions for half an hour or so..
GeorgF knows most about phylogeny and (multiple) alignment.

ClareS says "we're very grateful for your taking the time to talk to us - I remember only too well what writing a thesis was like"

Fulvio says "I would like to know if owl db is avalaible for any user "

ClareS says "the owl database is available from several sites"

ClareS says "unless it's changed since the last time I used it, access from th UCL page is free and unrestricted"
ClareS will try it again today, tho', as these things change all the time

ClareS says "yes - OWL is there."

ClareS says "the URL is"

ClareS says "OWL is an excellent database - really well annotated. The only problem is that it isn't being kept up to date"
Who [guest] materializes out of thin air.

Fulvio says "it seems faster than swiss-prot"

Who [guest] [to Hello] Clare!
Who [guest] -)))

ClareS [to who] who are you IRL?

ClareS says "the latest version of OWL is version 31.1, created end 1998, but this isn't keeping pace with the source databases"

Who [guest] says "im Alinafrom Poland""
DavidM finds his way in.

ClareS says "it depends what you're interested in.. you will be able to work with Owl unless you need to study very recent sequences. Then even Swissprot won't be good enough. You will have to go back to translations of the source (DNA) databases like TrEMBL"

ClareS says "welcome, Alina and David"
DavidM sorry I'm late

ClareS says "are you clear about the difference between SwissProt and TrEMBL?"

AndyS says "no"

Fulvio says "yes"

ClareS says "SwissProt is a well annotated, comperhensive database of proteins which generally have been well characterised"

Who [guest] says "Can u read"Can u read me, Clare?""

Fulvio says "TrEMBL is a db of translated protein"

GeorgF says "yeah, the net is kinda slow. A nice list of databases (incl. OWL) is I just got it loaded-- the list is a little outdated already"

ClareS says "many new sequences won't make it into SwissProt for months, maybe years"

Who [guest] says "I wanna have "

ClareS [to who] I can read you fine

Who [guest] says ""I wanna have a name""

ClareS says "TrEMBL is a translation of the EMBL gene sequence database "

Who [guest] says "Don't wanna be a who""
GeorgF nods, but not all the translations may be valid protein

ClareS [to GeorgF] that's a useful URL - but it is *very* difficult to keep all these resource lists up to date, the Net changes *very* fast

Fulvio says "Are all the swiss-prot's entry also in TrEMBL?"

Who [guest] says "sure, thanksa lot""

ClareS [to Fulvio] no, you will need to search SwissProt and TrEMBL together to search all sequences...

ClareS says "currently SwissProt has 77977 entries and TrEMBL has 179091 entries"

ClareS says "you will sometimes see references to a database called SPTR. This means SwpssProt+TrEMBL together"

Nada says "There are weekly! updates to swissprot and trembl, which are on most SRS servers"

ClareS says "updates to the main DNA sequence databases are daily"

ClareS says "in a lot of bioinfo projects you will find that you have to *keep on* searching the databases as new sequences of interest will (may) be appearing all the time "

ClareS says "do you know about Swiss-Shop?"
ClareS looks round expectantly

GeorgF says "In TrEMBL, they try to mark those translated EMBL sequences that are ``not coding for real proteins''-- see But still, these are all just heuristics until you've ``seen'' the protein in vivo / in vitro.."

Fulvio says "help"

ClareS [to Fulvio] what would you like help on / with?

Fulvio says "I think I've lost the connection"

ClareS [to Fulvio] you're OK - can you read this?

Who [guest] says "R u from Portugal, Fulvio?""
GeorgF solicits more questions, especially on phylogeny and alignment-- gotta continue my thesis in 10 minutes..

Fulvio says ",ClareS, I am here again"

ClareS says "anyone with a question for Georg? " ClareS [to georg]: I've got one for you: I'd appreciate your opinion on matrices - which onnes do you regard as"best" for local and global alignment?

Fulvio says "Is possible to force an alignment taking into consideration secondary structure ?"

ClareS [to Fulvio] good question ClareS [to Fulvio]: that is one reason why it is *not* good, except in trivial cases, just to take an alignment obtained automatically with a program like Clustal "as read"

ClareS says "there are several good alignment editors around which allow you to manipulate a sequence alignment by hand"

Fulvio says "In fact I know that the better way to align a sequence is often manually..."

ClareS says "one of the best uses for that is to alter an alignment to take secondary structure into account"

This is the last thing I heard about the issueTo quote Gotoh (1996)
``[...] the order of superiority of GCB250 > Blosum62 > JTT250
>= MDM250 appears definite''. (MDM250 is another name for Dayhoff's
original Mutation Data Matrix.) See ``Table 2'' on page 827 of Gotoh, O. (1996) "Significant improvement in accuracy of multiple protein
sequence alignments by iterative refinement as assessed by reference to structural alignments." J. Mol. Biol. 264, 823-838.

GeorgF says "GCB250 is the matrix referenced as Gonnet, Cohen and Benner, Science 256, 1443-1445, 1992."

GeorgF says "Blosum62 is the matrix described in Henikoff and Henikoff, PNAS 89, 10915-10919, 1992;"

ClareS says "I usually start with an automatic alignment and tidy it up manually, Manual sequence alignment from scratch is a very time consuming and tedious business"

ClareS says "There's an alignment editor in GCG, and Cinema (available from the UCL site) is an interesting Java-based one"

ClareS [to georg] thanks very much - useful information and references

GeorgF says "So at least for global alignment, I'd use GCB250 as the matrix (but check whether something better has been published last year or so. "

Global multiple alignment module that allows the alignment of protein
primary structures as well as tertiary structures..

ClareS [to GeorgF] do you know how this matrix was determined?

GeorgF says "GCB250 is an improvement over MDM250, but I don't know the details."

GeorgF says "There may be some more links -re- alignments taking secondary structure into account, at"
GeorgF starts waving...
ClareS has just tried that French URL and it crashed Netscap
ClareS . o O ( crashed Netscape, of course... )

Who [guest] says "Bye, GeorgF!""

Who [guest] says "See ya!""

GeorgF [to ClareS] has just tried that French URL and it crashed Netscap

GeorgF [to ClareS] yeah, that page has $#@$#@#@#$ Java...
ClareS normally has few problems running Java
GeorgF waves, has to leave..

Fulvio says "I am trying german url but I arrived on a coursebook"

GeorgF [to Fulvio] You should arrive at a list of Multiple Alignment resources...

ClareS [to GeorgF] thanks very much for coming.. greatly appreciated!

ClareS [to GeorgF] will you ba able to join us to-morrow night?

Fulvio says "thank you very much, GeorgeF"
ClareS reloads Netscape..

GeorgF thanks ClareS for inviting him, and waves one last time)
KLaurio finds his way in.
(KLaurio has disconnected.)

ClareS [to KLaurio] Hi, welcome - but I'm afraid that you're 1h late.
ClareS . o O ( line problems? )
GeorgF goes home.

ClareS says "that URL of Georg's is very useful - a very full explanation of multiple alighnment"

ClareS says "it's considerably more complex than the level of knowledge required for PPS, tho', so if it fazes you you should just ignore it.."

Fulvio says " ClareS the french one or the german one?"

ClareS [to Fulvio] sorry, the German one

ClareS says "again.."
GeorgF materializes out of thin air.
GeorgF nods, I should be page'able tomorrow, too.
GeorgF goes home.

Who [guest] says "Is anyone there?""

ClareS says "the french one should be a useful resource but its Java seems to be dodgy"
(Who [guest] has disconnected.)

Fulvio says "last year I used one my own sequence both with multalin and clustalw, and the results were different!"

Nada says "mmm that does look very useful!"

ClareS [to Fulvio] how different were the results?

Fulvio says "the programs seemed tho weight in different way a substitution"

ClareS [to Fulvio] alignments will depend on the matrices you use - if the programs used different matrices you can expect (slight) differences in the alignment

Fulvio says "i lost completely an inserction of 8 residues..."
The housekeeper arrives to cart KLaurio off to bed.

ClareS says "this is another reason why it's not advisable to trust automatic alignment absolutely"

ClareS says "the programs only consider sequences as characters with particular relationships between them, they know nothing of the biology"

Fulvio says "both program were not able to locate the inserction and fragmentating the rest of the sequence they tryied to align my protein"

ClareS says "there are sometimes several answers with very similar theoretical "weights""

Fulvio says "sorry for my english, i know it is terrible..."
(AndyS has disconnected.)
Alina [guest] materializes out of thin air.

ClareS says "you will sometimes, at least, be able to pick the "correct" alignment *only* by knowing the biology"

ClareS says "sorry, the MOO seems to have crashed: (if you see this) it's probably a good time to leave. Thanks for making it an interesting meeting"
ClareS turns the ClareS_recorder off.