[Arabidopsis] Updates to the BAR - Botany Array Resource - March 2006

Nicholas Provart provart at botany.utoronto.ca
Wed Mar 8 17:50:16 EST 2006


Hello everyone,

We have updated and upgraded the Botany Array Resource at
http://bbc.botany.utoronto.ca, with the following:

1. Final version of the electronic Fluorescent Protein (eFP) Browser
released, with a new URL at
http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi or linked from the BAR
homepage above. Thanks to everyone who suggested improvements, and thanks
again to Detlef Weigel and colleagues for generating the Gene Expression Map
of Arabidopsis Development (Schmid et al., 2005, Nature Genetics 37:501-506)
upon which the eFP Browser is based.

2. Expression Angler custom bait feature introduced. This is *really* useful
for the identification of tissue-, condition-, or mutant-specific genes.
Simply design a "bait" that is just "on" in your sample of interest, and
pull out all the genes that match that pattern. Use these to get promoters,
or as condition-specific PCR markers.

3. Affymetrix ATH1 probe set to AGI number lookup table updated, based on
the TAIR Genome Release 6.0 (TAIR6). Previous lookup tables are now
searchable with the "_at to AGI converter" at
http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_agi_converter.cgi. 

4. Beta-version of MarkerTracker released. Genome-wide predicted CAPS
markers across 96 Arabidopsis accessions (based on Magnus Nordborg's ecotype
data, published in Aranzana et al., 2005, PLoS Genetics 1:e60), for
leveraging the power of natural variation in gene discovery studies.
Feedback requested. Available at
http://bbc.botany.utoronto.ca/markertracker/ 

5. Significant upgrades to the "DataMetaFormatter" introduced, to improve
exploration of Arabidopsis microarray data in the outputs of Expression
Browser, ExpressionAngler and other programs listed available at the BAR.

6. Bug fix for BlastDigester for newer NCBI Blast and Bl2Seq outputs, for
designing your own CAPS markers based on ecotype-specific sequence you may
have generated.

Feedback is always welcome,

Best regards,

Nick
.........................................
Nicholas Provart, Ph.D.
Assistant Professor, Plant Bioinformatics.
Faculty Member, Program in Proteomics and Bioinformatics.
Rm 3051, Dept. of Botany, University of Toronto.
25 Willcocks St., Toronto, ON. M5S 3B2. CANADA.

Tel. (+1) (416) 978-7141, Fax. (+1) (425) 675-7036
URL. http://www.botany.utoronto.ca/faculty/provart/
Webtools. http://bbc.botany.utoronto.ca   
email. provart at botany.utoronto.ca
TTC. Spadina LRT, Willcocks St.




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