Maize Genome Assembly (730,000 GSS)

Patrick S Schnable schnable at iastate.edu
Wed Nov 5 18:13:53 EST 2003


Dear Maize Genetics Community:

The Consortium for Maize Genomics 
(https://www.fastlane.nsf.gov/servlet/showaward?award=0221536) and 
other groups have deposited hundred of thousands of maize genomic 
sequences in Genbank. I am very pleased to announce the release of an 
assembly of over 730,000 of these sequences (127 MB). This assembly 
(version 2.3.1) contains 94,000 contigs (MAGIs) with an average 
length of 1.3 kb and 4 GSSs/contig. It was generated by a 
collaborative research group that includes members of the Aluru, 
Ashlock and Schnable labs at Iowa State University using funding from 
NSF and ISU.

You may access the assembly at 
http://www.plantgenomics.iastate.edu/maize. This site allows you to 
BLAST your favorite gene or cDNA against the assembled contigs of 
GSSs.

We've been very pleased with the coverage; almost all genes that 
we've BLASTED detect one or more substantial segments of assembled 
genomic sequence. We therefore decided to make this assembly 
immediately available to the community even though our current Maize 
Genome Assembly website is still a "bare bones" operation. Because we 
plan to substantially enhance this site over the next several months 
(and generate a new and improved assembly), we welcome your comments, 
suggestions and feedback.

Finally, I'd like to invite you to attend a talk on our assembly 
pipeline that will be presented by graduate student Scott Emrich 
January 12th at the PAG meeting 
(http://www.intl-pag.org/12/12-bioinformatics.html).

-Pat

-- 

Patrick S. Schnable
Director, Center for Plant Genomics
Professor of Plant Genetics
2035B Roy J Carver Co-Lab
Iowa State University
Ames, IA  50011-3650 USA

schnable at iastate.edu
515-294-0975 (office)
515-294-7209 (administrative assistant)
515-294-5256 (fax)
http://schnablelab.plantgenomics.iastate.edu






More information about the Maize mailing list