[Bioperl-l] Indexing large databases / BioSQL

Sendu Bala bix at sendu.me.uk
Mon Apr 7 08:34:00 EDT 2008

Bánk Beszteri wrote:
> Hi Hilmar,
> it was important to understand that the inconsistency in taxon names is 
> apparently only between the Swissprot entries with "non-standard" names 
> and the contents of the taxonomy tables and that it is best to use a 
> pre-loaded taxonomy, thanks for that! We have now updated to 
> bioperl-live (and bp-db-live, too) and load_seqdatabase.pl seems to have 
> loaded everything OK in ~26 hours (with many of the "The supplied 
> lineage does not start near..." warnings, but no other problems).

Can you provide some examples of these warnings (of the taxons that 
cause them)? If there's anything consistent about them perhaps 
Bio::Species can be improved to accommodate them properly (instead of 
just issuing the warning and getting the classification wrong).

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