`gene` glyph and implied UTRs

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`gene` glyph and implied UTRs

Robert Buels
Hi all,

Bio::Graphics::Glyph::gene bills itself in its POD as 'a GFF3-compatible
gene glyph', but it doesn't seem to support UTRs that are implied by the
differences between the CDS and exon features ("implied UTRs"), which in
the GFF3 spec seems to be the canonical way to represent them.

This seems like it should be fixed, probably just by having the glyph
*not* ignore implied_utrs and adjust_exons.

Lincoln, does that sound like the right thing to to?  I can volunteer to
do it if so.

Rob

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Re: `gene` glyph and implied UTRs

Keiran Raine
Hi Rob,

Can you clarify if this issue is the likely cause of the missing end  
to the third transcript (KRAS) in the attached image?  The gene data  
was converted from Ensembl GTF using the code packaged with GBrowse.




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Thanks,

Keiran Raine
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The Cancer Genome Project
Ext: 7703
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On 9 Sep 2011, at 19:56, Robert Buels wrote:

> Hi all,
>
> Bio::Graphics::Glyph::gene bills itself in its POD as 'a GFF3-
> compatible
> gene glyph', but it doesn't seem to support UTRs that are implied by  
> the
> differences between the CDS and exon features ("implied UTRs"),  
> which in
> the GFF3 spec seems to be the canonical way to represent them.
>
> This seems like it should be fixed, probably just by having the glyph
> *not* ignore implied_utrs and adjust_exons.
>
> Lincoln, does that sound like the right thing to to?  I can  
> volunteer to
> do it if so.
>
> Rob
>
> ------------------------------------------------------------------------------
> Why Cloud-Based Security and Archiving Make Sense
> Osterman Research conducted this study that outlines how and why cloud
> computing security and archiving is rapidly being adopted across the  
> IT
> space for its ease of implementation, lower cost, and increased
> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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Re: `gene` glyph and implied UTRs

Robert Buels
On 09/10/2011 10:31 AM, Keiran Raine wrote:
> Can you clarify if this issue is the likely cause of the missing end to
> the third transcript (KRAS) in the attached image? The gene data was
> converted from Ensembl GTF using the code packaged with GBrowse.

It could be, the symptoms of this that I've been seeing are that the UTR
regions of exons are 'dropped', leaving weird dangling intron connectors.

Attached is an example of one of my GFF3-canonical gene's alternative
transcripts, drawn first with the gene glyph, and then with
processed_transcript with implied_introns turned on.  It looks similar
to what you're seeing.

Rob


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Re: `gene` glyph and implied UTRs

Fields, Christopher J
On Sep 10, 2011, at 2:55 PM, Robert Buels wrote:

> On 09/10/2011 10:31 AM, Keiran Raine wrote:
>> Can you clarify if this issue is the likely cause of the missing end to
>> the third transcript (KRAS) in the attached image? The gene data was
>> converted from Ensembl GTF using the code packaged with GBrowse.
>
> It could be, the symptoms of this that I've been seeing are that the UTR regions of exons are 'dropped', leaving weird dangling intron connectors.
>
> Attached is an example of one of my GFF3-canonical gene's alternative transcripts, drawn first with the gene glyph, and then with processed_transcript with implied_introns turned on.  It looks similar to what you're seeing.
>
> Rob

I have seen the same thing with some of our local honey bee data, but solved it by explicitly generating UTR regions.  So, I think Rob's diagnosis is correct, implied UTRs are not currently supported.  However, would a 'best practice' be to explicitly define these, or leave them implied?

chris


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Re: `gene` glyph and implied UTRs

Robert Buels
On 09/10/2011 01:05 PM, Fields, Christopher J wrote:
> I have seen the same thing with some of our local honey bee data, but solved it by explicitly generating UTR regions.  So, I think Rob's diagnosis is correct, implied UTRs are not currently supported.  However, would a 'best practice' be to explicitly define these, or leave them implied?

Well, the GFF3 spec says to leave them implied.  So if that's not the
'best practice', the GFF3 spec would need to be changed.

I don't have a strong opinion on it one way or the other, my only strong
opinion is for consistency.

Rob

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Re: `gene` glyph and implied UTRs

Fields, Christopher J
On Sep 12, 2011, at 12:20 PM, Robert Buels wrote:

> On 09/10/2011 01:05 PM, Fields, Christopher J wrote:
>> I have seen the same thing with some of our local honey bee data, but solved it by explicitly generating UTR regions.  So, I think Rob's diagnosis is correct, implied UTRs are not currently supported.  However, would a 'best practice' be to explicitly define these, or leave them implied?
>
> Well, the GFF3 spec says to leave them implied.  So if that's not the 'best practice', the GFF3 spec would need to be changed.
>
> I don't have a strong opinion on it one way or the other, my only strong opinion is for consistency.
>
> Rob

+1.  Even if TIMTOWTDI, consistency is good.  Pointing that out on the GFF best practices page is a good idea.

chris
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Re: `gene` glyph and implied UTRs

Robert Buels
On 09/12/2011 10:37 AM, Fields, Christopher J wrote:
> On Sep 12, 2011, at 12:20 PM, Robert Buels wrote:
>> Well, the GFF3 spec says to leave them implied.  So if that's not the 'best practice', the GFF3 spec would need to be changed.
> +1.  Even if TIMTOWTDI, consistency is good.  Pointing that out on the GFF best practices page is a good idea.

To be clear, by "GFF3 Spec", I mean the 'The Canonical Gene' section of
the GFF3 specification at http://www.sequenceontology.org/gff3.shtml

Rob

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