wEST-SQL Database

The links below connect to a relational database containing EST, Contig, and Mapping information, including data of the NSF DBI-9975989 project efforts. This along with other tools has been developed to assist tracking of ESTs being used as probes for mapping to the wheat genome. Other queries may be obtained from the GrainGenes database at the GG2 Quick Queries Page, or at the GG2 Advanced Query Pages.


GrainGenes Database and Companion Resources


BLAST Databases

These databases are maintained locally and serve local research activities. Custom databases are set up to screen against Triticeae sequences, Assemblies, cDNA libraries, and other specialty formatted databases.


The wEST resource is a USDA-ARS sponsored server of nucleic acid sequence data for Triticeae-associated research projects located at the USDA-ARS Western Regional Research Center, Albany, California. Other associated projects which use resources located at this site are:


wEST Tracefile Server

This location holds the sequencing records for many of the ESTs maintained in the wEST database. Listed are the sequencing dates, plate numer (which is important for library identification), and the quality of the sequencing run. Since many of these samples were run on the ABI 3700 and CEQ 2000 automated sequencers, results are shown for 96-member lots. Also available here are the FASTA and Quality files for the run (this is untrimmed data).


Triticeae Sequence Data

Last download: April 24, 2003

General Queries


Software and Links

Computer processing of sequence data
SQPR: Sequence Quality Plate Reader
Triticeae Repeat Database Resource
GIRI Repeat Database Resource


Development Projects

Many of the new tools added to the databases are first tested at the development machine located at Cornell University, Ithaca, NY. As new ideas and requests for viewing data are suggested, they are developed and tested here.


Ongoing Projects

Wheat mapping via chromosome deletions, tool unique to wheat.

EST Classes

A short listing of some of the types of ESTs identified

EST Methodology

Clone Generation with GeneMachines oxygenated shaker
DNA purification by Biomek 2000
Sequencing by ABI 310, CEQ 2000, (ABI 3700)
Computer processing of sequence data
Animation of capillary sequencing. by Jason Chang

GrainGenes Probe Repository

A collection of mapped probes annotated in the GrainGenes Database Project are available for distribution. Many of these probes are cDNAs from cereals which have been sequenced and added to the EST database. For more information, please visit the GrainGenes Probe Repository

Reports


E-mail inquiries to: curator@wheat.pw.usda.gov