help: abstract genome - gene finder

Kevin Karplus karplus at cheep.cse.ucsc.edu
Tue Mar 9 08:14:02 EST 2004


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 bit
> 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 Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.





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