[BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .

[Steve Lianoglou]

Hi,

On Sun, Oct 28, 2012 at 12:01 AM, Holly <xyang2 at uchicago.edu> wrote:
> Steve,
>
> As the motif I am interested is [AAGTTTAA].
> Then I got a result on the negative strand as chr3:49450073-49450080,
> [GGTGAGGC], which is reversely complementary to [AAGCCTCA].
>
> Should I compare the reversely complementary hit to the motif?

Well -- think about your protein of interest as it binds to the DNA.
Do you think it's important which strand the protein is binding to?

Does your protein only bind single stranded DNA?

> If a hit is on a positive strand, then to compare the hit directly to the
> motif?

I'm not sure what you're asking here, but again -- I'm guessing the
biological scenario you are trying to model is when the DNA is paired
w/ its cognate/opposite strand and you are scanning for some
transcription factor binding site ... so I guess it's worth asking
yourself if the strand that "the correct" sequence motif is on is
important here.

> Say, a literature review/database gives the motif by default for a positive
> strand?

I'm not actually sure what the consensus (if there is one) for which
strand to use in order to report the motif in such databases.

-- 
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