help: abstract genome - gene finder

Raf rafta4NO^spam at hotmail.com
Tue Mar 9 08:17:48 EST 2004

we've had a chat with our professor,
and it was like u said, no read proteins in it, just in each genome 4
regions that were artificial genes
luckely these four genes have an equal length in each genome so now aligning
them is simple

the purpose of the assignment was to get a small introduction into
to let us use some of the tools available on the internet etc

tnx for all your help :)



"Kevin Karplus" <karplus at cheep.cse.ucsc.edu> wrote in message
news:slrnc49i65.sf7.karplus at cheep.cse.ucsc.edu...
> In article <sC21c.19949$Kj2.1082460 at phobos.telenet-ops.be>, Raf wrote:
> > we dont know what type of species it is...
> > its supposed to be a 'complete abstract genome of 1000 bp', so thats a
> > short for being vertebrate DNA..., but u never know...
> At only 1000 bp, it's short even for a viral genome.  You may not have
> any real proteins in it, so the appproaches of looking for known
> proteins may not help you.  They probably wanted you to do all-vs-all
> alignment with your other tiny genome to find conserved regions and
> make a synteny map.  In viral genomes, generally almost every open
> reading frame is expressed---even when the ORFs overlap in different
> frames.
> Quite frankly, I don't think I like the idea of an open-ended
> assignment based on fake data where knowledge of the biology can't be
> applied and the standard techniques of the field are not applicable.
> You have to guess what model the professor used to fake the data, and
> design a tool to fit that model---not really a very useful skill,
> particularly if the model is a poor one.
> It would be different if the assignment were using REAL data.
> --
> Kevin Karplus karplus at soe.ucsc.edu http://www.soe.ucsc.edu/~karplus
> Professor of Biomolecular Engineering, University of California, Santa
> Undergraduate and Graduate Director, Bioinformatics
> Affiliations for identification only.

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