[Genquire-users] more bug fixes to Genquire

[Mark Wilkinson]

Just a quick note that the Genbank flat file data adapter is functioning
much better now, and exports FASTA/GFF that can be read into a Genquire
native database using the GFF import plugin.

Unfortunately, BioPerl does not (IMO) export valid GFF2 format - I fixed
this BioPerl bug more than a year ago, but it looks like someone un-did
my fix to compensate for their own GFF2 format quirks :-/    Grrrrr!

Anyway, it still works so long as you stay inside of the
BioPerl/Genquire environment, so that's all that matters to us.

There are a few small changes to the Genquire database schema that can
be executed on a full database without corrupting it.  These changes
*must* be made for the new CVS codebase and released versions to work. 
In the Admin subfolder there is a 3.2 to 3.4 conversion SQL that will do
it for you :-)  The most significant change is that assemblies now have
a column for assembly_name, and that name will appear in the GenomeMap
window in place of the chromosome name.  This change was made in
particular for those of you using Genquire to hold small genomes like
bacteria or viruses, where you want to have multiple strains of the
beastie in a single database to facilitate 1:1 comparisons - the name of
the strain can now appear above the relevant contig (it used to be a
cryptic "chr 1", "chr 2", etc. by default).  The name, sadly, must be
entered by hand into the db for the moment, but it's better than nothing
:-)

Oh!  And just for fun, and as a nod of congratulations to the BCGSC in
Vancouver for being "the first" to get an assembly, there are now two
copies of the SARS Coronavirus sequence in the DEMO database.  I ran an
InterProScan on one of them (the BCGSC assembly) last night and imported
the results into the database.  The second was an import of another
isolate that I picked up from Genbank this morning and imported it using
the methodology I describe above.

Cheers all!

Mark


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