PlantGDB BLAST

Step 1: Select the databases to be searched You can select more than one. For example you can search 'All plants' EST and 'Zea mays' GSS and 'Glycine max' PUT.
Database Shortcuts
Arabidopsis thaliana genome
Oryza sativa genome
Zea mays GSS
Sorghum bicolor GSS
Zea Mays BAC
Other Databases
Barley1 GeneChip Exemplars
Zea mays RFLP's
Organism Groups:
 
Species name:
« « « Begin typing to search ... a drop down box should appear with your query
Organism Transcript PUT GSS STS HTG other_DNA Protein
Step 2: Select which type of BLAST to run

Now, paste your query sequence into the large text field or upload your query sequence file. You may enter up to 100 query sequences at one time.

Sequence name (optional) Program E-value

Paste query sequence(s) in FASTA format OR paste query sequence ID(s):

Or upload up to 100 query sequence(s) in FASTA format OR a file of up to 100 sequence ID(s):

Advanced Parameters

Optional Step: Refine your BLAST query using Advanced Blast parameters.

Filter Matrix Word size
Cost to open a gap Cost to extend a gap
Threshold for extending hits
Perfom gapped alignent {not available with tblastx}
Length of the largest intron allowed in tblastn for linking HSPs
X dropoff value for gapped alignment (in bits)
X dropoff value for ungapped extensions (in bits)
Penalty for a nucleotide mismatch (blastn only)
Reward for a nucleotide match (blastn only)
Number of database sequences to show one-line descriptions for (V)
Number of database sequence to show alignments for (B)
Query Genetic code to use
DB Genetic code (for tblast[nx] only)
Number of processors to use
Effective length of the database (use zero for the real size)
0 for multiple hit, 1 for single hit (does not apply to blastn)
Query strands to search against database (for blast[nx], and tblastx)
X dropoff value for final gapped alignment in bits (0.0 invokes default behavior) blastn/megablast 50, tblastx 0, all others 25
MegaBlast search
Frame shift penalty (OOF algorithm for blastx)
Step 3: Submit your BLAST job