[Genome] reverse!

Robert Kuhn kuhn at soe.ucsc.edu
Mon Feb 27 16:38:55 PST 2006 

 Hi, Tim,

 I'd like to add to what Fan sent you this morning.  I've interspersed 
 my comments among quotes from your messages.

> I read a couple discussion threads that refer to an arrow near
> the base position track when it is in Full diplay mode, but I
> don't see any arrow on which to click.
> OK, I found the arrow (don't know why it wasn't there before),

  In order to see the reverse sequence arrow in the Base Position
  track, it must be in "full" display mode, as you found, and it must
  also be zoomed in at least close enough that the Browser can display 
  codons as separate vertical bars (roungly one pixel per codon).  You 
  may have found it by zooming in without realizing that this is what 
  made it visible.

> but the protein translation is still not complemented,

  The protein translation for an annotation track such as Known Genes
  is given in the direction of transciption, as indicated by the
  arrows in introns in the Browser display. (We have checked the amino
  acid sequence against NCBI for ABCC6 just to be sure, and confirmed
  that we are displaying the correct AA sequence).  Complementing the
  DNA sequence in the Base Position track does not affect the translation
  display in an annotation track.

> [when the Base Position arrow is reversed] The DNA sequence reads the
> correct strand, but reads 3' to 5',

  Your observation is correct.  A click on the arrow at the left of the Base
  Position track will complement the DNA sequence (and the three-frame
  translation), but does not reverse it.  That means that the DNA and
  AA sequences must be read from right to left (in the direction
  indicated by the arrow).  Here is a region in an intron of your ABCC6
  gene in the hg17 assembly with ATGs in both directions.  The methionines
  that would be translated from it are easily picked out by the green color:

    chr16:16,183,656-16,183,739

  Note that they change when you click the arrow.

> Isn't there a way to display my reverse-strand gene in a
> left-to-right (5' to 3') orientation?

  A 5'-to-3' display on the negative strand within the Genome Browser is
  not supported.  We always display the reference sequence and annotations
  using the NCBI convention with Base 1 and the p-arm of the chromosome on 
  the left.  Fan's suggestion of using the Proteome Browser for the
  exons of Known Genes is the only place to find that.

> Anti-intuitive, and difficult to work with.

  Perhaps.  The strandedness issue gives us and many of our users
  headaches, I'll agree!  The alternative would have been to reverse
  the entire browser display when the Base Position arrow was reversed.
  We decided that this would have confused things even more when using
  the <<<, <<, < and >, >>, >>> and other navigation controls.

  We appreciate your interest in the Browser and would be happy to
  entertain suggestions for improvements in our display.  Many features
  and modifications have been made as the result of user input such as
  yours.

  best wishes,
 			--b0b kuhn
 			ucsc genome bioinformatics group

> From genome-bounces at soe.ucsc.edu  Mon Feb 27 09:02:23 2006
> To: "Hefferon, Timothy \(NIH/NHGRI\) [E]" <thefferon at mail.nih.gov>,
>         <genome at soe.ucsc.edu>
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> Subject: Re: [Genome] reverse!
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> Hi Tim,
> 
> If you click on the gene (assuming you are using the UCSC Known Genes (KG)
> track),
> you will see the KG details page, click "Proteome Browser" in the Quick
> Links section
> will bring you to the Proteome Browser, in which the exons and protein are
> always
> displayed from 5' to 3' with DNA sequences of both directions displayed (if
> it
> is a "-" strand).
> 
> Fan.
> -----Original Message-----
> From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
> Behalf Of Hefferon, Timothy (NIH/NHGRI) [E]
> Sent: Monday, February 27, 2006 8:35 AM
> To: genome at soe.ucsc.edu
> Subject: Re: [Genome] reverse!
> 
> 
> OK, now I'm getting uncomfortable.  The DNA sequence reads the correct
> strand, but reads 3' to 5', so the DNA sequence I am looking at, reading
> left to right, doesn't actually exist!  I.e., an example splice site reading
> 5' to 3' is, CCCTTTCTCTCAG-exon.  What I see in the browser is
> exon-GACTCTCTTTCCC.  Anti-intuitive, and difficult to work with.
> 
> Isn't there a way to display my reverse-strand gene in a left-to-right (5'
> to 3') orientation?
> 
> Thanks,
> Tim
> 
> 
> -----Original Message-----
> From: Hefferon, Timothy (NIH/NHGRI) [E]
> Sent: Mon 2/27/2006 11:33 AM
> To: Hefferon, Timothy (NIH/NHGRI) [E]; genome at soe.ucsc.edu
> Subject: RE: reverse!
> 
> OK, I found the arrow (don't know why it wasn't there before), but the
> protein translation is still not complemented, so it's completely useless -
> 3 frames in the wrong orientation.  Any ideas?
> 
> Thanks,
> Tim
> 
> 
> -----Original Message-----
> From: Hefferon, Timothy (NIH/NHGRI) [E]
> Sent: Mon 2/27/2006 11:29 AM
> To: genome at soe.ucsc.edu
> Subject: reverse!
> 
> 
> Hi,
> 
> I bet you get this one a lot, but I couldn't find a straightforward answer
> in the FAQ.
> 
> I work with a gene that happens to be on the minus strand (ABCC6 on chr16).
> When I look at it in the Genome Browser, it goes from right to left.
> Problem is, when I look at the sequence - for example, to examine splice
> sites, GT-AG - everything is the reverse complement of what I want to see,
> including protein translation.  I read a couple discussion threads that
> refer to an arrow near the base position track when it is in Full diplay
> mode, but I don't see any arrow on which to click.
> 
> Please help!
> 
> Thanks,
> Tim
> 
> 
> 
> 
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