Markers not quite in gramene

[Steven Schmidt]

The reason for this problem was that some markers were missing their
HELP tags.  I added these and also HELP tags for the Sequence objects
that were missing them.

(Database changes were made to gramene-dev on brie2.  Also,
the Gramene Ensembl pages on gruyere now link to the development version
of
Gramene.)

Following Doreen's instructions, I checked that the markers
from the JRGP 2000 study were in gramene-dev properly:

Of the 3267 markers
1799 have Marker_type=RFLP, Type=RFLP   as expected
1288 have Marker_type=RFLP, Type undefined
 118 have Marker_type=RFLP, Type=RAPD
   3 have Marker_type=RFLP, Type=Morphological, namely Ph, alk, Rc
   1 has Marker_type undefined, Type=RAPD, namely P169

2227 had no Enzyme
It looks like P60, for example should have no enzyme:
http://bank.dna.affrc.go.jp:80/cgi-bin/dbrun/RiceDB?find+Locus+%22P60%22

All markers were connected to a Locus on the  Rice-RGP-2000  MapStudy.

1305 markers had no Locus that began marker_name-hyphen
    as they do on Rice-BS125/WLO2-2000-(RC00), the
    Rice-Nipponbare/Kasalath 1994 & 1998 studies, etc.
Some of these may be like G24A and G24B which have the same sequence
as G24.  G24A and G24B have Loci only on Rice-RGP-2000, while
G24 has G24-11RJ94, among others.
Do we consider these as one marker, G24, or two, G24A on R11 and G24B on
R12 ?
Either way we have to fix the data- G24 has loci on both.

 130 markers were missing some of the Related_Sequence's
I added these, referring to existing Sequence objects where possible,
otherwise creating the Sequence objects.

101 Sequence's were created
with DB_info
and without Raw_seq
The added Sequence names have the "gb:" prefix

Some sequences, such as D15092, occur both with and
without the "gb:" prefix
Some sequences associated with markers have DNA or Raw_seq and some
don't.
Some have     External_DB_Key DDBJ/EMBL/GenBank ...
instead of     DB_info Database GenBank  ...

I guess these things will be cleaned up in the process of dumping
and loading into Oracle.


I noticed that the gramene/map/marker page showed only one
related sequence and changed it to show all of them.


Should I add whatever Raw_seq is missing for Sequence's
associated with these Markers?

-Steve





Steven Schmidt wrote:

> If you go to simple search in gramene and enter
> C523A or E4392S or E885S or E4483S
> and then click on the marker link, you get a blank page.
>
> This marker link is what I'm going to from contigview
> (e.g.
> http://www.gramene.org/gramene/map/marker?name=E4392S&class=Marker
> )
> It works for plenty of markers.
>
> --
> Steven Schmidt
> snp.cshl.org     www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977