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

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Jun 8 17:16:51 CEST 2010


>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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