Update sequence?

Jean Thierry-Mieg mieg at ncbi.nlm.nih.gov
Fri Dec 1 04:22:54 EST 2000


There is a call in the acedb kernel to automatically
update all coordinates in touched objects up and down the hierarchy
provided they are declared withe the modifier COORD in the
ace model

however, this call is not included in any public interface
and my self i never use it
so i cannot garantee the reliability, but i beleive it works

this means that to use this call you would have to write some c
code

if there is demand, you could trigger the interest of the cambridge
group to add that public interface but just now, i could not 
spare the needed time for this, sorry

jean
>To: bionet-software-acedb at moderators.isc.org
>From: Keith Bradnam <keith at thale.life.nottingham.ac.uk>
>Subject: Re: Update sequence?
>Mime-Version: 1.0
>X-Trace: oyez.ccc.nottingham.ac.uk 974805477 13264 128.243.116.150 (21 Nov 2000 
11:17:57 GMT)
>X-Complaints-To: usenet at news.nottingham.ac.uk
>NNTP-Posting-Date: 21 Nov 2000 11:17:57 GMT
>To: JRSchwartz at lbl.gov
>X-Sender: keith at thale
>Date: Tue, 21 Nov 2000 15:58:15 +0000 (GMT)
>
>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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