Recent improvements at UK CropNet

Keith Bradnam keith at thale.life.nottingham.ac.uk
Thu Feb 8 10:04:40 EST 2001



We, the UK Crop Plant Bioinformatics Network (UK CropNet), have recently
been making some useful additions and improvements to our website
(http://ukcrop.net). A brief summary:


New database
------------
We now have kindly been granted permission to mirror the CompositDB
database (from UC Davis) to supplement the existing 31 plant-related
databases on our site (see http://ukcrop.net/db.html).  This is a database
for the Compositae species and currently focuses on Lettuce and Sunflower.



Improvements to AGR
-------------------
The Arabidopsis Genome Resource (AGR - http://ukcrop.net/agr) has been
expanded to also include EMBL sequences and annotations from 20 different
Arabidopsis species/subspecies.  In addition to containing *all*
Arabidopsis sequences from EMBL, AGR contains SwissProt+TREMBL protein
sequences and annotation from *all* higher plant sequences (all of which
have been BLAST-searched against the Arabidopsis genome sequence).

External database links have now been added to the InterPro, Pfam,
PROSITE, PRINTS, and Mendel-GFDb databases.  Links have also been added to
the NCBI's taxonomy website and links are currently been added to PubMed
to allow searching of paper abstracts.



Improved BLAST server
---------------------
You can BLAST search against all of the sequence-containing databases on
the UK CropNet server by going to http://ukcrop.net/perl/ace/ncbi_blast

For our arabidopsis database, AGR, you can search against separate,
specialised, BLAST databases. E.g.

Only search against AGI clones from chromosome 'x'
Search against full length chromosome sequence from chromosome 'y'



Insert BLAST server for Arabidopsis
-----------------------------------
You can also search your Arabidopsis gene-of-interest against our database
of insert sequences to see if you can order a potential knock-out line
from NASC (see http://arabidopsis.org.uk/blast.html).

Furthermore, you can register your sequence with our free 'InsertWatch'
facility (http://arabidopsis.org.uk/insertwatch) and we will let you know
as soon as a potential knock-out line becomes available (NASC are
expecting many 1000's of new insert lines to become available this year).



Feedback and comments about our website/databases are especially welcome!

Keith

~  Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and
~  Arabidopsis Genome Resource  (http://ukcrop.net/agr) developer.
~
~  Nottingham Arabidopsis Stock Centre, University Park,
~  University of Nottingham, NG7 2RD, UK.  Tel: (0115) 951 3091




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