Ancient origins found in arabidopsis genome


o USDA-ARS Center for Agricultural Bioinformatics at Cornell: http://genome.cornell.edu/index.html

How Cornell's computing resources help to "blast" against databases

Running a massive BLAST search on the Arabidopsis genome was easier for Cornell University researcher Todd Vision than it might have been for many other genomics researchers, thanks to the Cornell Theory Center (CTC). The center maintains a special computing resource in Rhodes Hall on the Cornell campus in conjunction with the U.S. Department of Agriculture's Center for Agricultural Bioinformatics (CAB).

The resource, loosely named the 'genomics cluster,' consists of 12 computers, each made up of four 500-Mhz Pentium III processors running the Windows 2000 operating system. With software developed for CTC, eight of the machines run as a parallel-processing cluster, effectively a supercomputer.

The cluster is primarily used for searches using BLAST (an acronym for Basic Local Alignment Search Tool), a program that searches gene and protein databases for pattern matches, much the same way a text searcher will match words and phrases. BLAST servers are available elsewhere to the worldwide research community through World Wide Web interfaces, but they are not suitable for running a large batch of queries such as the one Vision used to track the genetic history of Arabidopsis .

The BLAST server on the Web takes one query and "blasts" it against the database, Vision explained. "But I needed to run twenty-something thousand proteins. Imagine sitting there and clicking the mouse that many times. Doing it on Theory Center computers allowed us to do it in a batch. Doing it all on local computers allows you more speed, more flexibility and less hands-on processing."

Vision also assembled on a Theory Center computer a specia

Contact: Blaine P. Friedlander Jr.
Cornell University News Service

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