[Biopython] comparing micro array data

Tue Mar 16 16:56:06 UTC 2010

If you need to visualize the microarray data and also do some analysis for
interaction networks, then 'Cytoscape' is a good option to go for.

Thanks
Subho

On Tue, Mar 16, 2010 at 12:00 PM, <biopython-request at lists.open-bio.org>wrote:

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> Today's Topics:
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>   1. comparing micro array data (Vincent Davis)
>   2. Re: comparing micro array data (Peter)
>   3. Re: comparing micro array data (Vincent Davis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 16 Mar 2010 09:03:45 -0600
> From: Vincent Davis <vincent at vincentdavis.net>
> Subject: [Biopython] comparing micro array data
> To: biopython <biopython at lists.open-bio.org>
> Message-ID:
>        <77e831101003160803n24a4568aq68793a367059f956 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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 ?
>
> Thanks
>
> *Vincent Davis
> 720-301-3003 *
> vincent at vincentdavis.net
>  my blog <http://vincentdavis.net> |
> LinkedIn<http://www.linkedin.com/in/vincentdavis>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 16 Mar 2010 15:15:27 +0000
> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] comparing micro array data
> To: Vincent Davis <vincent at vincentdavis.net>
> Cc: biopython <biopython at lists.open-bio.org>
> Message-ID:
>        <320fb6e01003160815s1e051330ve62211d6c7843f64 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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/
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 16 Mar 2010 09:30:42 -0600
> From: Vincent Davis <vincent at vincentdavis.net>
> Subject: Re: [Biopython] comparing micro array data
> To: Peter <biopython at maubp.freeserve.co.uk>
> Cc: biopython <biopython at lists.open-bio.org>
> Message-ID:
>        <77e831101003160830m4e679fa0v21df651d79db582a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> >
> > @Peter
>
> 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/
>
>
> I am working at getting up to speed with R and bioconductor. I ask the
> question here as I got such a great answer for the last question I had and
> thought if the tool was available in biopython then I would try it. I don't
> know how this problem is normally solved.
>
>
> <http://www.bioconductor.org/>
>
> >
>
>  *Vincent Davis
> 720-301-3003 *
> vincent at vincentdavis.net
>  my blog <http://vincentdavis.net> |
> LinkedIn<http://www.linkedin.com/in/vincentdavis>
>
>
> On Tue, Mar 16, 2010 at 9:15 AM, Peter <biopython at maubp.freeserve.co.uk
> >wrote:
>
> > 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/
> >
>
>
> ------------------------------
>
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> End of Biopython Digest, Vol 87, Issue 16
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>

-- 
Subhodeep Moitra
First Year, Masters Student
Language Technologies Institute
School of Computer Science
Carnegie Mellon University
Pittsburgh, PA , USA