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

[Steve Lianoglou]

Hi,

On Sat, Oct 27, 2012 at 10:54 PM, Holly <xyang2 at uchicago.edu> wrote:
> Hi, Steve,
> Thank you.

No problem.

[snip]

>  More question is, to screen the "promoter" region, what should I do?
> Should I focus on the "upstream" of "positive" strand? Does it equally to
> search the "downstream" of "negative" strand, if the program reports
> sequence of only negative strain?

Sorry, I don't follow your question.

The promoter of a gene/transcript is "defined" as some region *around*
the transcription start site. I say "around" instead of "upstream"
because people often/occasionally/might-be-inclined-to include
sequence up to and including the first intron of a gene when looking
for regulatory motifs.

That having been said, a standard/run-of-the-mill analysis might start
by simply focusing on sequence *upstream* from the TSS. You don't go
"downtream" of a negative strand ... the region I pointed you to look
at for your sequence motif is still *upstream* of the gene, even
though you are moving "to the rightt" on the sequence.

You don't orient upstream and downstream by something being left or
right of a position ... these terms are relative to the strand of
transcription. So for features located on the positive strand, you
"look left" for "upstream. Genes annotated on the negative strand,
their upstream region is "to the right"

I'm not sure if that what you were asking, but I hope it's helpful and
made some sense.same.

-steve

-- 
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