[Biopython] comparing micro array data

[Peter]

On Tue, Mar 16, 2010 at 3:03 PM, Vincent Davis <vincent at vincentdavis.net> wrote:
> So I am very new to this so please accept my ignorance on this subject.
>
> I have several micro array samples ~ 8 for each of 3 known genomes. So I
> know which probes/sequences are a match and which have close matches. I
> would like to identify which sequences exist in an unknown sample. The array
> is custom and there is little to know overlap between probes.
> What is the "standard" way of doing this? I don't care to know if a SNP is
> present only if the sequence is present.
> Is this standard available in biopython ?

Hi Vincent,

Biopython has only limited pairwise alignment built in - we normally just
call specialised command line tools. In addition to classic microarray
probe design tools, you *might* be able to exploit related tools for PCR
primers or short read tools from next generation sequencing. However,
these won't be specifically aware of microarray probe affinities and how
to model them.

For microarray work I would have to say using R/Bioconductor will
probably be more sensible for the very practical reason that they
have a much larger community using microarrays than Python does.
http://www.bioconductor.org/

Peter

P.S. You can call R from Python, see http://rpy.sourceforge.net/