[DAS] How to represent variations on DAS?

[Lincoln Stein]

Hi Linus,

For deletions, you can represent the deletion as its endpoints.  For 
insertions, you can provide a 0 bp range and then give the inserted sequence 
as a <target>.  For substitutions, you can provide a region equal to the size 
of the substitution, and then give the alternate sequence as the <target>.

Lincoln


On Tuesday 15 April 2003 09:41 pm, Linus Taejoon Kwon wrote:
> Hi,
>
> Is it possible to represent the variation/mutation information using DAS?
>
> I think that it's not easy to use DAS protocol for
>
>  (1) indel site (how can I define the position of insertion?)
>  (2) the alternative sequence information
>
> If the documents related to this issue, please let me know.
> (I cannot find any clues in current DAS/1 Sepc. and DAS/2 RFCs)
>
> Regards,
>
> Taejoon Kwon
> linusben (at) bawi (dot) org
> _______________________________________________
> DAS mailing list
> DAS at biodas.org
> http://biodas.org/mailman/listinfo/das

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================