[BioC] ProbeID: how to find which one is close to 3 prime end of DNA- help,

Saurin D. Jani saurin_jani at yahoo.com
Tue Jun 8 18:09:24 CEST 2010

Thanks Steve and Kevin,

so, I got coordinates of probe sequence alignments then if strand is (+) then take largest "start" number and if strand is (-) then take smallest start number which gives me closest position of probes on 3 prime end. 


--- On Tue, 6/8/10, Steve Lianoglou <mailinglist.honeypot at gmail.com> wrote:

> From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
> Subject: Re: [BioC] ProbeID: how to find which one is close to 3 prime end of  DNA- help,
> To: saurin_jani at yahoo.com
> Cc: "bioconductor" <bioconductor at stat.math.ethz.ch>
> Date: Tuesday, June 8, 2010, 11:16 AM
> Hi,
> >Could you please let me know, how can I find out from
> given list of ProbeIDs:
> >
> > Which Probe's location is close to 3 Prime END of
> DNA?
> If you don't mind doing a little programming, you could
> also:
> 1. get the probe sequences for your array (there are
> bioconductor
> packages for these too)
> 2. realign them
> 3. check where the land on your "genes" by getting familiar
> with the
> GenomicFeatures package.
> > How its different....if location is mapped to POSITIVE
> or Negative Strand?
> In all likelihood it probably won't matter since I'm pretty
> sure most
> array protocols require (at some point) amplification of
> the material
> that will be hybridized to the chip, which will lose any
> strand info
> of the molecules in your sample.
> I could be mistaken, though, so you might want to read up
> on the
> details of your experiment, or perhaps wait for others to
> chime in.
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact

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