Comparative mapping in acedb

Ed Griffiths edgrif at sanger.ac.uk
Fri Jun 13 04:59:33 EST 2003


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 |

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