[DAS] Configuring a valid MAPMASTER?

[Chris Cole]

Hi Andy,

Thanks for the help. Looks like I was close...

I now get an error regarding the 'types' command. I haven't implemented 
it so that's not a surprise. However, I'm struggling to find 
documentation on the build_types() function and what data it should 
return. My source data only has one type: 'expression_tag' so how should 
I return that?
Cheers,

Chris

On 07/02/11 11:40, Andy Jenkinson wrote:
> Hi Chris,
>
> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>
> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>
> (assuming thaliana)
>
> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>
> Cheers,
> Andy
>
> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>
>> Hi,
>>
>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>
>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>> http://plants.ensembl.org/das/dsn
>> Or am I barking up the wrong tree?
>>
>> Any pointers much appreciated.
>> Cheers,
>>
>> Chris
>>
>>
>> _______________________________________________
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>


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Dr Chris Cole
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