I think you have a big problem

[David Horner]

Dear Gramene

I think you may have a big problem with the labelling (and linking) of 
your Barley TIGR GI clusters.

If you perform a blast search (with a barley est as probe) against this 
database, you recover the same hit as at the TIGR site (in terms of the 
pairwise alignment identified by the BLAST search). However, the 
contigs are labelled differently to those at TIGR. If you then follow 
the link to the construction of the contig, the sequence you recover 
bears NO RELATION AT ALL to the one that the BLAST search identified. 
In fact, these are invariably RICE sequences rather than barley 
(although NON HOMOLOGOUS to the initial probe or blast hit).

The problem may be as simple as the linking of names to sequences in 
the database, but it is a bit of a pain in the arse to find that a lot 
of work put into identifying contigs is completely invalid.

Hope this information is useful, If I am mistaken in my identification 
of a database compilation problem I apologise (and would be glad to 
understand how I have misused your site). In the meantime I will 
continue my work at TIGR.

regards

David






Dr David S. Horner

Horner's Five Thumb Postulate: Experience varies directly with 
equipment ruined.

Dipartimento di Scienze Biomolecolari e Biotecnologie
University of Milan
via Celoria, 26   -  20133 Milano, Italy
Tel. (+39) 02 50314916
Fax (+39) 02 50314912
e-mail:  david.horner at unimi.it


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