[DAS] How to represent variations on DAS?

Lincoln Stein lstein at cshl.org
Thu Apr 17 10:05:14 EDT 2003

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>.


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

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