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Comparative mapping in acedb

Keith Bradnam krb at sanger.ac.uk
Fri Jun 13 10:45:27 EST 2003


Hi Martien,

>From your error message it looks like it is expecting some value to the
right of a tag called 'Fish' in your map object ('CGA1').  Is there a tag
called 'Fish' in the 'CGA1' Map object?

Keith


On 13 Jun 2003, Ed Griffiths wrote:

> All,
>
> I have received the below note from Martien (please reply to the newsgroup or
> him directly) about setting up comparative mapping in acedb. I have not used
> this facility, to save me wading through code etc., can anyone help Martien to
> get this going ?
>
> thanks Ed
>
> > From: "Groenen, Martien" <Martien.Groenen at wur.nl>
> > Subject: AceDB Comparative mapping
> >
> > Dear Ed,
> > As you might remember, I have been using AceDB for several years now for our chicken
> > mapping data.
> > I now also would like to use the comparative mapping features build into acedb.
> > Unfortunately, the models for how to organise the input data is not so well documented
> > and so far I haven't been able to get it working.
> > I have tried the following.
> > I have made two Map_sets one for the chicken chromosomes and one for the human
> > chromosomes:
> > Map_set chicken
> > Map GGA1
> > Map GGA2
> > Etc.
> > Map_set Human
> > HSA1
> > HSA2
> > Etc.
> > I also made a homology_group to link the human and chicken orthologs:
> > Homology_group
> > Pairwise locus1chick locus1hsa
> > Pairwise locus2chick locus2hsa
> > Etc.
> > I also tried the following option which also did not work:
> > Locus Locus1
> > Map GGA1 position 25
> > Map HSA1 position 78
> > When I choose Oxgrid in the comparative map chooser I get the following error message
> > (several times for every map combination) :
> > Sorry, unrecognized expression to the right of FOLLOW: {Find Map GGA1;>Fish} SETAND {
> > Find Map HSA1;>Fish} Should be FOLLOW tag or FOLLOW tag#tag
> > Eventually the last message I get is " Sorry no homologies for these Map_sets"
> > Could you tell me what I am doing wrong?
> > If possible, do you have a full description of the models and all tags for the classes
> > Map_sets and Homology_group or any class I am not aware of that is needed for the
> > comparative mapping option.
> > (Or alternatively you might have an acedump from a working database which is using these
> > features?).
> > Best regards,
> > Martien
> >
> > Martien Groenen
> > Animal Breeding and Genetics Group
> > Wageningen University
> > The Netherlands
>
> --
>  ------------------------------------------------------------------------
> | 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 |
>  ------------------------------------------------------------------------
>
>

~  Keith Bradnam - WormBase group: http://www.wormbase.org/
~
~  The Wellcome Trust Sanger Institute,
~  Hinxton, Cambridge, CB10 1SA, UK.  Tel: 01223 494922






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