Getting the gene from the pseudo gene

Kevin Karplus karplus at cheep.cse.ucsc.edu
Mon Mar 8 13:03:55 EST 2004


In article <c27dlq$1qmqc7$1 at ID-154800.news.uni-berlin.de>, Colossus wrote:
> I have a list of homo sapiens pseudo gene retrieved
> from GenBank database. I would like to know how
> to get the gene from which the pseudo gene "was
> extracted". I'm trying to blast the nucleotide's pseudo
> gene sequence but many are the result who come out.
> Since I want to automatize the process of collecting the genes
> from the pseudo ones it's not possible to estabilish a criteria
> for retrieving the gene through an automated process (a Perl script)
> by having so many and different result, so my question is:
> 
> Is there a database around on the web that giving the sequence or
> the accession number of the pseudo gene gives ONLY one gene, the
> UNIQUE gene from which the pseudo one was extracted ?

I believe that there is a pseudogene track on the browser at
http://genome.ucsc.edu, but I've not used it, so I don't know how much
information it carries.

I think that your question is a bit difficult to answer.  For example,
there are many active copies of many of the RNA genes.  There are also
many RNA pseudogenes.  Separating the active genes from the
pseudogenes is already ery difficult, but trying to identify which of
the many identical or near-identical copies the pseudogene came from?
It may be easier for genes that have unique copies, but I was under
the impression (perhaps mistaken---this is not my field) that
processed pseudogenes occured mainly for highly expressed genes that
often had high copy numbers to begin with.

If my understanding is correct, then what you ask for is not really possible.
The best we could do is to cluster the pseudogenes and genes, and say
that a paticular pseudogene comes from a particular cluster of genes.
One may even have different levels of clustering, with the set of
possible genes getting wider as the pseudogene decays through
non-selective mutation.

As always, I welcome correction---I have only 3rd hand knowledge of
pseudogenes and may have garbled what I was told.

-- 
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.




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