dna_homol in sequence class

Dave Matthews matthews at greengenes.cit.cornell.edu
Tue Sep 3 03:38:44 EST 2002


Hi Richard,

Yes the operation of moving rightward in AQL is tricky.  In this case,
change your query,

select a, a[4], a[5] from a in object ("sequence", "Em:AC104662")->DNA_homol where a = "Mm_A:contig_66209"

to

select a, start, start[1] from a in object ("sequence", "Em:AC104662")->DNA_homol, start in a[4] where a = "Mm_A:contig_66209"

This gives the desired three rows.

- Dave

> To: bionet-software-acedb at net.bio.net
> From: Richard.Adams at ed.ac.uk (Richard Adams)
> Subject: dna_homol in sequence class
> Date: Fri, 30 Aug 2002 09:36:14 +0100 (BST)
> 
> Hello,
> 
> I'm trying to get the genomic sequence coordinates for the start/finish
> of DNA homology matches to particular BACS in our in-house Ace database.
> 
> My AQL query is
> 
> 
>  select a, a[4], a[5] from a in object ("sequence",
> "Em:AC104662")->DNA_homol where a = "Mm_A:contig_66209"
> 
> where a[4] is the start coord and a[5] the end coord. But, for a
> sequence (say a cDNA ) with multiple matches, this doesn't return say
> 
> name    23    345
> name  567    789
> name 1024    4567
> 
> which is what I would like,  instead it returns
> 
> name 23 345
> name 23 789
> name23 4567
> name 567 345
> name 567 789
> name 567 4567
> name 1024    345
> name 567 789
> name 1024    4567
> 
> Can anyone help me on this? If there is just a single match this query
> works fine. Likewise if I just ask for a[4] or a[5] I get just three
> rows returned.  In the data model there doesn't appear to be any nested
> data structure
> for multiple matches but as I 'm a bit new to all this there may be a
> totally obvious answer, in which case my apologies.
> 
> Thank you for your time,
> 
> 
> Dr Richard Adams
> Molecular Medicine Centre
> University of Edinburgh
> richard.adams at ed.ac.uk
---





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