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

[Artemus Harper]

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
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