[DAS2] Example alignments

Ed Griffiths edgrif at sanger.ac.uk
Wed Jun 7 15:35:56 UTC 2006


> I'm truly sorry at how long it has taken me to get these examples to you. I
> hope that the example alignments in the enclosure makes sense to you.
> Unfortunately I found that I had to add a new "target" attribute to <LOC> in
> order to make the cigar string semantics unambiguous. Otherwise you wouldn't
> be able to tell how to interpret the gaps.

I think your idea of having a common "role" is a good one but I wondered if we 
could use the term "query" for the sequence that is to be aligned (i.e. the EST 
in your example) and "subject" for the reference sequence ?

I also wondered why the hsp hits could not be nested within the overall 
alignment tags ?...probably that is opening a whole can of worms though....


| Ed Griffiths, Acedb development, Informatics Group,                    |
|  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
|  Hinxton, Cambridge CB10 1HH                                           |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |

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