[Bioperl-l] Re: How to retrieve the unigene number

[P B]

Hi all,

This is post from May 9th about how to get a UniGene cluster ID given the 
genbank accession.  The answer suggests using the ClusterIO and Unigene 
modules to do the parsing step.  I also read the threads a while back about 
the development of these modules, and it sounds exactly like what I need.

So... where do I find them?! :)

They don't seem to have come with my 1.02 distribution, nor are they 
included in the documentation for that release.  Is there a place where I 
could get my hands on the code?

It's probably in an obvious place I didn't look, eh?
Tats

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Giuseppe Torelli wrote:

>I'm a newbie regarding Bio Perl and also Perl. I've followed the discussion
>about the unigene module;
>would you please tell me how to retrieve the unigene number of a gene
>knowing the GenBank
>accession number ?

Hi Giuseppe,

I'm sure there is "more than one way to do it" but here are a couple. Which
you use depends on how often you want to look up a unigene from an accession
number.

1. If it is just once or twice, I would just visit the UniGene website,
select the appropriate organism, type in the acc number and hit search.

2. If you wanted to do lots of this I would:
- download the appropriate organism file from UniGene ie. Hs.data
-  use the ClusterIO and Unigene modules to parse the file (this takes some
time, I leave mine overnight)
- drop the resulting data into a SQL db
- search on acc number to get back to the UniGene no
- the ClusterIO/Unigene modules can parse right into the seq lines so you
can pull out all the acc numbers for each unigene.
- you could then write a perl script that did the retrieval for all the acc
numbers you are interested in (especially say if there are thousands of
them).

I hope this helps...

Cheers, Andrew.

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