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TIGR Rice Genome Annotation Project - Web BLAST Server
 

The TIGR Rice Genome Project BLAST server has a collection of databases for use in searching with the BLAST programs blastn, blastx, tblastn, or tblastx. There are a total of 24 databases to search. You can find a detailed explanation of the databases here.

The TIGR Rice Pseudomolecules database allows users to search against the latest version of the 12 TIGR rice pseudomolecules. There are three additional databases for searching the Release 4 pseudomolecules: Genes in TIGR Rice Pseudomolecules:Genomic sequences, Genes in TIGR Rice Pseudomolecules:CDSs, and Genes in TIGR Rice Pseudomolecules:Protein sequences.

Databases also available include Rice, Barley, Maize, Rye, Sorghum, Sugarcane, and Wheat TIGR Gene Indices, TIGR Maize Assemblies(5.0), TIGR Sorghum MF Assemblies, KOME Full Length CDNAs, all Rice BAC and PAC sequences in Genbank, TIGR Oryza Repeat Database, TIGR Gramineae Reapeat Database, Rice Marker Sequences, Rice BAC end sequences, Flanking Sequence Tags, and three databases from the TAIR Arabidopsis Annotation Release 6.

The annotated sequences include both experimentally characterized genes and those based on gene predictions. Click here for information regarding the annotation of rice genes at TIGR.


This server runs WU-BLAST 2.0. [Disclaimer]
Select a program and database to search against:

Program:
Database: Alignments:
Upload a file containing a sequence OR paste it into the textbox:
(Note: If both are entered, the file will be ignored.)
Enter the name of the file containing a sequence in FASTA or raw format:
Enter your sequence in FASTA or raw format:
Sequence identifier (for definition line if raw sequence entered):


Options:
Matrix: Filter: Expect:
Cutoff: Strand: Descriptions:
Wordlength (for blastn only): Echofilter Ignore Hypotheticals
Graphical Overview Map Overview PID (map overview only)


The email option allows the user to be notified by email when the blast search is completed. The email will contain a link to the results. Use this option when running a lengthy search. To activate this option, check the box to the left and fill in an email address in the box to the right.
Send a link to results to email address:


 
 
 
 
For Rice Comments/Questions send mail to the TIGR rice team.
 
Photographs courtesy of Robin Buell (TIGR), Jiming Jiang (University of Wisconsin), and the USDA Agricultural Research Service