x-rated acedb

Jean Thierry-Mieg mieg at ncbi.nlm.nih.gov
Fri Sep 22 12:50:12 EST 2000

acedb recognisez the upac code

n is sometimes shown as - in displays

w, s etc are recognized and used by acedb in numerous cases
like in non matching ovelapping cosmids

x is NOT a UPAC letter

so this whole letter is just creating confusion
and should have been removed by the moderator

jean thierry-mieg

>To: bionet-software-acedb at moderators.isc.org
>From: Keith Bradnam <keith at thale.life.nottingham.ac.uk>
>Subject: x-rated acedb
>Mime-Version: 1.0
>X-Trace: oyez.ccc.nottingham.ac.uk 969554819 8030 (21 Sep 2000 
16:46:59 GMT)
>X-Complaints-To: usenet at news.nottingham.ac.uk
>NNTP-Posting-Date: 21 Sep 2000 16:46:59 GMT
>X-Sender: keith at thale
>Date: Fri, 22 Sep 2000 08:19:04 +0100 (BST)
>Hi all,
>I've just discovered that tf you read a sequence into Acedb which contains
>an 'x' (representing an unspecified base) it seems to convert it into an
>insertion ('-').  It also messes up the format of the sequence in tree display
>(at least in AceBrowser).
>I know that 'N's are 'allowed' by acedb, but this made me start thinking
>whether acedb recognises any of the other internationally agreed symbols,
>e.g. 'w' for weak (A or T) etc.
>Anyone know any more about this - is acedb just misbehaving here, or is
>there any sort of reason for converting 'x' into '-'???
>~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
>~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
>~  University Park, University of Nottingham, NG7 2RD, UK
>~  Tel: (0115) 951 3091 

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