How to view overlapping sequences

Keith Bradnam keith at thale.life.nottingham.ac.uk
Tue Nov 9 13:23:11 EST 1999


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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