Your name(s) : Joe White (Christoph Benning, John Ohlrogge)

Department and campus address : 219 Biochemistry
Telephone and email address : 353-1999, whitejo@pilot.msu.edu
Title of talk & presenter : Bioinformatics for the Seed EST functional
genomics project.

Abstract:

	Large scale sequencing and expression analysis (functional
	genomics) of Arabidopsis thaliana genes are important
	experimental methods for the Arabidopsis Functional Genomics
	Consortium.  Our laboratory is studying seed specific genes in
	wild type and seed metabolic mutants of Arabidopsis, with the
	goal of identifying genetic factors controlling storage
	compound accumulation in developing oil seeds. These will be
	targets for future attempts to improve oil crops by Metabolic
	Engineering.  

	A total of 11,068 cDNAs (ESTs) from a normalized developing
	seed library of Arabidopsis have been partially sequenced from
	the 5’-end. A MS Access97 database has been established
	which maintains data from more than 9900 BLAST search results,
	and which will be the basis for further Bioinformatic
	Analysis.   

	The data from the BLAST searches has been used to select ESTs
	for inclusion in microarrays.  Selected ESTs were PCR
	amplified for preparation of DNA microarrays.  An array
	containing 525 elements printed in quadruplicate was
	simultaneously hybridized with cDNA from leaves or roots.  The
	goal of this work is to identify the putative function for
	seed specific ESTs.  The BLAST data will be linked with
	results from microarray analyses to putatively identify
	individual ESTs of interest that are spotted on an microarray.  

	Software tools developed for this project include PERL scripts
	designed to 1) automatically launch BLAST or FASTA searches
	and archive the results, 2) process sequence files in GCG and
	FASTA format, and 3) parse BLAST and FASTA search result
	files.  Development of the database is nearing completion.