[Gmod-help] Re: [Gmod-gbrowse] Glyph 'dna' display problem

[Artemus Harper]

I am looking for a way to show primers at the nucleotide level with the enhancers marked as such and any part that doesn't match all the reference sequences highlighted (this also means I need to show multiple reference sequences, although I can probably hide the true reference sequence).
On Apr 30, 2010, at 11:18 AM, Scott Cain wrote:

> Hi Artemus,
> 
> I'm not sure I understand: the dna glyph is only really usable for the
> reference sequence (ie, the chromosome or whatever the other features
> a drawn in reference to).  Other glyphs like generic and segments know
> how to draw dna when zoomed in.  Is that what you want?
> 
> Scott
> 
> 
> On Fri, Apr 30, 2010 at 2:09 PM, Artemus Harper <subanark at gmail.com> wrote:
>> Ok, I updated to the newest version of gbowse (the new version is at:
>> http://vm-gmod.eecs.wsu.edu/cgi-bin/gb2/gbrowse/primer2/?start=253;stop=352;ref=genome;width=800;version=100;flip=0;grid=1;id=1ae82ac1261f191c48bd51641c91191a;label=DNA-Primer)
>> 
>> As you can see I am still seeing the same glyph problem.
>> 
>> On Mon, Apr 26, 2010 at 1:45 PM, Artemus Harper <subanark at gmail.com> wrote:
>>> 
>>> I do have an old version of Gbrowse (not sure how to determine my current
>>> version), I'm trying to update it right now, but I'm running into some
>>> issues. The install script says it cannot find CBuilder.pm, which I assume
>>> may be included in a newer version of perl I have installed (5.8.8) which
>>> according to the wiki is high enough to install with. I'll get perl updated
>>> once I resolve my conflict with the repos.
>>> 
>>> On Mon, Apr 26, 2010 at 12:49 PM, Dave Clements, GMOD Help Desk
>>> <help at gmod.org> wrote:
>>>> 
>>>> Hi Artemus,
>>>> I think you've found a bug.  The primers appear to only be correctly
>>>> aligned when the view includes the start point for the primer.  The code is
>>>> also showing too much DNA for the primers, making the primer DNA image be
>>>> too wide.
>>>> Does anyone have an idea on this, other than a coding bug?
>>>> Thanks,
>>>> Dave C.
>>>> 
>>>> 
>>>> On Fri, Apr 23, 2010 at 11:09 AM, Artemus Harper <subanark at gmail.com>
>>>> wrote:
>>>>> 
>>>>> I'm trying to use the glyph dna to see nucleotide sequences when you
>>>>> zoom in. However, this doesn't seem to be working for features. In
>>>>> particular, if a contig refers to a part of another contig, it isn't
>>>>> displaying the right data when the start of the sequence is not in view.
>>>>> 
>>>>> For example, I'm looking at one of my sequences starting at
>>>>> genome:470.570. I see:
>>>>> 
>>>>> <-----------------------------------------------
>>>>> 470
>>>>> DNA/GC Content
>>>>> tgtgatttctatgttatgta...
>>>>> 
>>>>> Primers
>>>>>    S4
>>>>>    gatttctatgttatgta...
>>>>> 
>>>>> But when I move over to the right:
>>>>> <-----------------------------------------------
>>>>> 500
>>>>> DNA/GC Content
>>>>> taagggcatatcggttgaag...
>>>>> 
>>>>> Primers
>>>>> S4
>>>>>  cgaagaaacaaattatattt...
>>>>> 
>>>>> which for S4 isn't what was displayed at 500, although it is for the
>>>>> genome sequence.
>>>>> 
>>>>> You can see this yourself (when the two tracks are turned on):
>>>>> http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:470..570
>>>>> and when shifted over:
>>>>> http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:500..600
>>>>> --
>>>>> Artemus Harper
>>>>> 
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> 
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> Gmod-gbrowse at lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>> 
>>>> 
>>>> 
>>>> 
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>>> 
>>> 
>>> 
>>> --
>>> Artemus Harper
>> 
>> 
>> 
>> --
>> Artemus Harper
>> 
>> ------------------------------------------------------------------------------
>> 
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>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research