[Gmod-help] Re: [Gmod-gbrowse] Glyph 'dna' display problem
Scott Cain
scott at scottcain.net
Fri Apr 30 16:16:13 EDT 2010
Hi Artemus,
Well, both strands would be (relatively) easy: you would just need two
features, one with a positive strand, one negative. Multiple
references though is a bit of a non-starter; you can't really do that,
though you could kind of approximate it with the same approach that
the SynView/PlasmoDB people used:
http://plasmodb.org/cgi-bin/gbrowse/plasmodb/?start=1205700;stop=1285700;ref=Pf3D7_11;width=800;version=100;cache=on;show_tooltips=on;grid=on;id=e582c9987caf3252fec88e845db66da1;label=AnnotatedGenes-EST-SyntenySpansVivaxMC-SyntenyGenesVivaxMC
Though I still don't know how you show mismatches to the "fake"
reference sequence.
Scott
On Fri, Apr 30, 2010 at 3:36 PM, Artemus Harper <subanark at gmail.com> wrote:
> Yes, except I need to display both strands for the EST glyph. I also need to show mismatch based on more than one reference sequence.
> On Apr 30, 2010, at 11:44 AM, Scott Cain wrote:
>
>> Hi Artemus,
>>
>> Do you want to do something like figure 18 in the tutorial:
>>
>> http://gmod.org/gbrowse-cgi/tutorial/tutorial.html#multiple_alignments
>>
>> Scott
>>
>>
>> On Fri, Apr 30, 2010 at 2:33 PM, Artemus Harper <subanark at gmail.com> wrote:
>>> 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
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> Gmod-gbrowse at lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D. scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>>> Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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