[DAS2] Example alignments

Lincoln Stein lstein at cshl.edu
Wed Jun 7 16:44:02 UTC 2006

Query and subject are rather BLAST-specific and don't apply to other 
techniques, such as whole genome alignments. How about using "reference" for 
the reference sequence and "non-reference" for the target?


On Wednesday 07 June 2006 11:35, Ed Griffiths wrote:
> Lincoln,
> > 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

Lincoln D. Stein
Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
SANDRA MICHELSEN, AT michelse at cshl.edu

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