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.