[Biopython] comparing micro array data

[Leighton Pritchard]

Hi,

On 16/03/2010 Tuesday, March 16, 17:29, "Peter"
<biopython at maubp.freeserve.co.uk> wrote:

> On Tue, Mar 16, 2010 at 4:56 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> 
>> If you don't mind a couple of questions, for curiosity sake, how big is the
>> genome of model organism?  And what size are the arrays, in terms of
>> probes?
> 
> Also, what kind of organism? e.g. Plant, animal, bacteria? This will
> make a difference for the number of papers you'll find doing this kind
> of thing in the literature.

And the type of analysis that's being done, too: human aCGH (lots of
references) tends to concentrate on copy number variation and SNP
identification, while bacterial aCGH (not so many) focuses largely on
presence/absence of putative orthologues.
 
> On Tue, Mar 16, 2010 at 4:49 PM, Vincent Davis  wrote:
>> I actually was brought into this project by a team from an university. They
>> know lots including that this is a difficult problem. They did not have any
>> references as to how others have solved this problem with whatever success
>> was possible. Since I know python, biopython has been my first choice to ask
>> other smart people :)
> 
> For a recent example using microarrays for cross-species comparison
> (aka microarray comparative genomic hybridisation) in bacteria you
> might want to read Leighton's paper (and the references within - which
> include work on humans):
> 
> http://www.ncbi.nlm.nih.gov/pubmed/19696881
> 
> You can probably guess why he asked if you were doing array CGH ;)

<grin>

And I was just about to blow my own trumpet, too ;)  If you've got any
questions that are specifically about the paper, I'm happy to take them
off-list.

L.


-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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