[Bioperl-l] sequence object with no sequence data

Hilmar Lapp hlapp at gmx.net
Wed Sep 13 09:39:02 EDT 2006


Interesting. No, you can't - length and also feature positions are  
measured in basepairs.

Having said that, I'm not sure off the top of my head at which places  
and whether at all it is checked that the positions are actually  
integers. So, so long as you make sure that you never ask the system  
for translating to basepair coordinates, providing cM could be worth  
a try if you're in an adventurous mood. I.e., make the length long  
enough that your highest cM number is still lower, and never ask for  
subsequences. Also, the system may check that for features the start  
is greater or equal to 1, so you may have to translate the  
coordinates by adding 1 if some of your markers are at <1cM.

	-hilmar

On Sep 13, 2006, at 9:26 AM, Nathan Haigh wrote:

> Hilmar Lapp wrote:
>> Yes you can, just make sure you set the length. I'm not sure though
>> what you mean by taking slices of it.
>>
>>     -hilmar
> One more related quick question:
>
> Is it possible to have a sequence length measured in different  
> units so
> that decimals could be used? In particular, I'm thinking of  
> centimorgans
> as units and I'd also like to be able to draw these sequences using
> Bio::Graphics.
>
> Thanks
> Nath
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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