🚀 go-pugleaf

In a recent message posted to this bulletin board by Mathews et al, they
say:

> Much of the scientific excitement in plant genomic mapping over the last year
> has been about the surprisingly high degree of synteny exhibited by
> relatively distantly related species, and now people want to put together
> inter-species databases in ACEDB. A problem that arises in doing this with
> regard to the multimap is that frequently the 'same' (homoeologous) gene or
> locus is called by different names in different species.  The multimap
> currently only connects common loci by keying on the fact that they are
> literally the same locus, i.e. they have the same name.

and suggest that a tag within the ?Locus object be used to determine
which loci are tied together in the Multimap.


It's a good idea. However, we have other dificulties with regard to homologous
data. There are some species which have homologous genes but the symbols
are exactly the same. For example, the human, cow and sheep nomenclature.
As you can imagine, trying to store information with the same key causes
quite a few problems. To get around this, Jo Dicks and myself decided to
use a species prefix for all homologous data and keep the actual symbol
as a Text tag.
Eg Locus : "HsABL"
   Symbol : "ABL"

   Locus : "BvABL"
   Symbol : "ABL"

In fact, if this is done, all data items within the database need to have a
species prefix. But when it comes to displaying the data (whether on the maps
or in the keySet) we only want the symbol for that individual species, not
the symbol with the species prefix.

I tried to modify the genetic map code to do this but there are problems.
Could someone help me fix my code or if enough people want this facility,
could Jean and the acedb team offically implement this please.

The data structure for handling data objects to be displayed on the genetic
map is the SEG. It usually consists of the object's key, a few flags and the
object's position. Instead of using the key to display the object's name
(ie gene symbol) I have tried using a character pointer from within the SEG
structure. In the gMapConvert routine, this is set to point to the text
defined by the Symbol Tag definition in the ?Locus object. (ie is a Text tag,
not ?Text tag.) If this is done and later on you try and retrieve the Symbol
text, the data is corrupted and appears scrambled.

This is a pity because the only alternative which I have found that works
is: for each data object on the genetic map, retrieve its data (ie create
an OBJ for it) and then find the relevant data within the object for display.
It slows the map display down considerably and I am sure there is a better
way.

How is one expected to get help with acedb problems? Do you use this
bulletin board, or do you email Jean directly?

Michelle Kirby     (email kirbym@uk.ac.mrc.har-rbu)
Jo Dicks           (email jld@uk.ac.ox.bioch)