Wheat EST Data

Welcome!! In this site, you will be able to browse and download all the available EST data from hexaploid wheat and other Triticeae species produced in this project. Other relevant information concerning EST data is also available.

Sequence Data

5' EST data

The following two sites contain all the 5' ESTs including the most current ones generated at Albany, CA.
  1. Raw Data is where all the unprocessed sequence data are located.
  2. Processed Data contains sequence data after low quality bases and vector sequences were trimmed off. For EST data processing, Please go to large-scale EST data processing protocol for details.

The 5' EST data are organized by cDNA library. For information on cDNA library names, tissue types, etc, please check cDNA Libraries. All the sequence data are in FASTA format. You can view individual EST files from each library generated from individual sequencing runs. If you would like to download all the ESTs from the same library, or all wheat ESTs or all rye ESTs, please go to the download site instead.

3' EST data

The 3' EST data were generated during the process of validating ESTs used as probes for Deletion Mapping project. You can go to the download site to get 3' EST data.

A list of 5' EST names and their matching 3' EST names and their genbank accession numbers is available here.

Quality Score Files and Trace Files

Information on getting trace files can be found here.

The quality score files generated by Phred analysis are available to access at the download site.

Download Triticeae EST data

The place to download bulk EST data and quality score files

Database Search and Query

Users can choose either ACEDB based database or wEST-SQL, a MySQL based relational database, using your preferred query method to get data.

BLAST against Triticeae EST Dataset

Local BLAST against EST dataset generated in this project

Overall Progress on EST Generation

Overall summary of the Wheat EST project

Other Wheat EST Data

Wheat EST contributed from other labs

Large-scale EST Processing Protocol

The protocol used for processing large-scale raw data including trimming off low quality sequences, and vector sequence filtering and removal.

GenBank Submission Information

All the processed ESTs have been submitted to GenBank at NCBI. The information on genbank accession number and dbEST number for all the ESTs can be accessed from GenBank Number site. The GenBank numbers are organized by libraries. The EST name used for GenBank submission has been modified slightly from the EST name used in the fasta file. The EST name in the fasta file represents (plate number)_(96-well plate position)_(384-well plate position)Z_(numbers and letters generated from sequencing machine). The EST name used for GenBank submission is WHE(plate number)_(96-well plate position)_(384-well plate position)Z(a designated letter for sequencing primer used).

Example: Albany EST name - 2221_A04_A07ZS5_022.ab1, GenBank EST name - WHE2221_A04_A07ZS.
Example: Albany EST name - 2257_A01_B01Z_002.ab1, GenBank EST name - WHE2257_A01_B01ZE.

Sequencing primers and their designated letters:

  1. BKrev - V
  2. M13 forward - M
  3. M13 reversed - R
  4. Oligo dT - O
  5. Stratagene's pBSK reversed - B
  6. Stratagene's SK - S
  7. Stragagene's KS - K
  8. Clontech's MMAD3' - A
  9. T3 - E
  10. T7 - T
  11. Oligo dT wobble primer (an equal mixture of (T)27A, (T)27G and (T)27C) - Y