[Bioperl-l] Bio::Graphics : To change scale color & sort and add direction to SeqFeature

Chris Fields cjfields at uiuc.edu
Mon Aug 13 16:24:15 UTC 2007

On Aug 13, 2007, at 10:01 AM, Sendu Bala wrote:

> Shameer Khadar wrote:
>>> However, do your binding sites really have a direction? That is,  
>>> do you
>>> really know which strand your transcription factor bound to?
>> Yes, these info we collated from various experimental datasets.
> Well, those datasets I'd like to see... What I was getting at is the
> strand probably isn't known at the experimental level, but to describe
> the site a strand has to be arbitrarily picked so you can write the
> sequence of the site down as a single string. Its probably the case  
> that
> the strand information you have is just the way it happened to be
> reported in the literature and has no biological meaning.

It's subjective.  I can think of several cases where strandedness  
does matter and has meaning.  If the motif is related to how the gene  
is transcribed or post-transcriptionally regulated, for instance;  
elements which indicate start of transcription (-10/-35 or any sigma- 
factor-related promoter element in prokaryotes), end of transcription  
(poly-A signal, transcription terminators), modulation of translation  
(SECIS, IRES), or conserved DNA motifs which are transcribed prior to  
regulation (RNA-binding proteins like IRE).


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