[Genquire-users] BIG genquire update to include genbank flat file adaptor layer

[Mark Wilkinson]

Hi everyone!

When you CVS update the next time you will find that you screen fills up with
changes :-)  I've been a busy boy!

All I really added was the Genbank Flat-file adaptor layer.  This should work
straight out-of-the-box as a read-only viewer of any genbank file.  Simply
select "Genbank_Flat" as the data source from the drop-down menu when you
start up Genquire, then select the file.

It has the following limitations:

(1) it displays only one sequence in a genbank file, so if your file contains
more than one... too bad!

(2) feature length is not being reported correctly when features are selected

(3) Genbank genes are not containers for their transcripts or exons.  This
isn't a problem with genquire, this is a problem with BioPerl's Genbank
parser.  I'm just too busy right now to write the code to make it better.

(4) it is read-only...  but that is my project for next week!  In principle,
it should be read/write, and able to write-back the data to a new Genbank
file.

(5)  I have no idea how badly it will respond if you start to annotate what
you see on the screen... remember, I only claim it to be read-only!!  You
have been warned ;-)

In addition, I wrote a small tutorial which covers some of the more important
things I noticed when creating the adaptor layer.  Remember that I have never
seen the adaptor layer myself until I jumped into it, so hopefully I am not
too "tainted" by my own familiarity with the rest of Genquire, and have
written something useful to the rest of you.  The notes are in
AdaptorAPI.pod, in the AdaptorDocs folder.

I'll keep working on this adaptor, and the documentation,  as I find time.
It is really bare-bones right now, but it works!

Cheers all!

M


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada