How to view overlapping sequences

Doug Smith dsmith at UCSD.EDU
Fri Nov 12 11:06:14 EST 1999


I would be interested in the answer to the following question by Keith.
We currently use the blastcl3 client in Perl scripts to do this sort
of thing.

Also, a question re Overlap_right and Overlap_left:
There is asymmetry here.  The ace_4.7g models have an Int for Overlap-right
but not one for Overlap_left.  This Int, the overlap to the next 'leftward'
sequence, eg a cosmid, is apparently used in Richard's LINK script to generate
composite sequences.

But ... is there more to this?
Why would users also not be interested in the overlap to a 'rightward'
sequence?
Are Overlap_right and Overlap_left 'magic tags' in some sense?

Thanks
  -Doug



>On Tue, 9 Nov 1999, Richard Durbin wrote:
>
>> Hello Keith,
>>
>> Aha, you ended up with AGR.  Congratulations.
>
>Thankyou, I started last Monday (which was the same day that I finally
>submitted my thesis).
>
>Thanks for the help.  I won't pretend that I've got to grips with Acedb
>yet (certainly not within a week).  I will hopefully be attending the
>ACEDB course in January and that will help.
>
>There is no urgent need for me to sort this out for the Arabidopsis
>database as there is still a lot of sequence information to come before it
>will be necessary to link things together.
>
>One more question though.  The overlap information stored in the
>Overlap_left and Overlap_right tags...does this come from the comment
>field of the GenBank/EMBL entries?  Without a lof of BLAST searchs I don't
>see how else you piece together which sequences overlap.  I'm therefore
>uncertain of how applicable this is to A. thaliana as from what I have
>seen so far, very few EMBL entries have information about how they
>overlap...which begs the questions as to how our database knows that they
>*do* overlap in the first place.
>
>I shall try and refrain from asking you too many questions before I've
>learnt a little more about ACEDB.
>
>Thanks again for your help.
>
>Keith
>
>~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
>~  University Park, University of Nottingham, NG7 2RD, UK
>~  Tel: (0115) 951 3091 Web: http://synteny.nott.ac.uk/
>
>---








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