transition to 4_9

Ed Griffiths edgrif at sanger.ac.uk
Tue Apr 9 04:29:40 EST 2002


> I have been using 4_8a for quite a while to do annotation, I use the
> sequence map display.  We just installed 4_9d.   This is a pretty
> specific question.  My hand-curated genes, called hand_built in methods,
> are supposed to be blue.  But only the introns are blue.  The exon boxes
> are arbitrarily purple.  Any thoughts on why this is?  (The other two
> are correctly colored.)
> Method : "hand_built"
> Colour   BLUE
> Show_up_strand
> Width    2.000000
> Right_priority   2.000000
> Show_text

OK, this is down to some changes made by me so I'll answer this....

People at Sanger used to represent a set of exons and the CDS within those exons
as two objects, the object representing the CDS was a subset of the larger set
of transcript exons.

They were getting fed up with having to maintain large numbers of exons and to
get round this and enable them to store just one object with the CDS marked
within the object I added some new code.

You can now have one Sequence object with Source_exons and the CDS tag set to
show where the CDS is within the source exons. You can colour the CDS separately
by setting a new method tag called CDS_colour to the colour you want the cds
section to be in, the default colour is purple.

I would guess that in your database you have the CDS tag set for all your
hand-curated genes, this will mean that by default all the exons will be purple
as you have seen. To rectify this all you have to do is to add the new
CDS_colour tag to your method objects giving it the _same_ colour as the colour
of your existing Colour tag in the methods:

Method : "hand_built"
Colour   BLUE
CDS_colour BLUE             <<<<<<< Add this line....
Width    2.000000
Right_priority   2.000000

(This was covered in the February 2001 newsletter, you can see old newsletters
at: http://www.acedb.org/winfo/Newsletters/)

> One more question.  When I use AceBrowser to access the sgifaceserver,
> and retrieve the sequence map of a gene, the right end of the ace
> display is being cut off.  Can I fix it?

Can you give an example ?  Without that I can't help.

cheers Ed

| Ed Griffiths, Acedb development, Informatics Group,                    |
|        Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,  |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |

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