Update sequence?

Keith Bradnam keith at thale.nott.ac.uk
Tue Nov 21 10:58:15 EST 2000


On 20 Nov 2000 JRSchwartz at lbl.gov wrote:

> 
> 
> Hi all,
> 
> I am using acedb for annotation.  I was wondering if there is a way to
> update the dna sequence for a clone, to add more to it, while preserving
> the existing annotations.  I have done it in the past by hand, changing
> all the froms and tos, but it is a royal pain.  Is there a nice way to
> do that?  If I just delete the DNA sequence and add the new one, will
> the annotation be automatically updated?

DNA sequences are usually specified as 'UNIQUE' objects in most acedb
databases, so if you try to read a new DNA sequence as part of an existing
Sequence object it should just replace the existing DNA sequence but not
change anything else.

E.g. if your sequence/clone object in your database is something like:


Sequence : "EMBL:AB006697"
DNA      "EMBL:AB006697" 80970
Version  "AB006697.1"
Database_date    "26-OCT-2000"
Species  "Arabidopsis thaliana"
Title    "Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MAH20."
Clone    "MAH20"


Then all you should have to do is put your new DNA sequence in an ace file
with the same name as that which already exists and read this into the
database.


Keith

~  Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and
~  Arabidopsis Genome Resource  (http://ukcrop.net/agr) developer.
~
~  Nottingham Arabidopsis Stock Centre, University Park,
~  University of Nottingham, NG7 2RD, UK.  Tel: (0115) 951 3091 









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