MaizeGDB BLAST

Paste your sequence into the large text field and enter its name (optional). Press the "Run BLAST" button to perform a blast search against sequences in the selected database. To learn more about NCBI blast, click here.

Note: You can also try the BLAST searches available at:
NCBI BLAST, for the latest sequence sets from GenBank!
A Mu Transposon Information Resource to find out whether your sequence has been tagged by Mu!
The MaizeGDB Cornsensus BLAST Page to search against the Cornsensus sequence set!
PANZEA BLAST, for evaluating diversity data

Data Sets To Choose From

Dataset	Description	Genome Browser
RefGen_v2	The maize pseudomolecules (B73 RefGen_v2)	RefGen_v2 Browser
RefGen_v2 Super Masked	B73 RefGen_v2 sequences for repeats (Freeling Lab).	RefGen_v2 Browser
RefGen_v1	The maize pseudomolecules (B73 RefGen_v1)	RefGen_v1 Browser
RefGen_v1 Masked	B73 RefGen_v1 masked for repeats (Maizesequence.org).	RefGen_v1 Browser
RefGen_v1 Super Masked	B73 RefGen_v1 sequences for repeats (Freeling Lab).	RefGen_v1 Browser
BACs	Maize BAC sequences.	BAC-based Browser
EST	Maize EST sequences.	BAC-based Browser
GSS	Maize GSS Sequences.	No Browser data
MaizeNucleotide	Other maize nucleotide sequences (Excluding EST and GSS).	No Browser data

Programs
blastn - Compares a nucleotide sequence to the nucleotide sequences in our database.
tblastn - Compares a protein sequence against the translated nucleotide sequences in our database.

MaizeGDB BLAST

Sequence name (optional)	Program	Database	E-value
	blastn tblastn	B73 RefGen_v2B73 RefGen_v2 Super MaskedB73 RefGen_v1B73 RefGen_v1 MaskedB73 RefGen_v1 Super MaskedBACs EST GSS MaizeNucleotide	0.0001 0.001 0.01 0.1 1
Speed up search results on RefGen_v1 and RefGen_v2:
Maximum number of chromosome sequences to display: All 1 2 3 4 5 6 7 8 9 10
Maximum number of hits per chromosome to display:    All 1 10 25 50 100 250
Sequence (raw or FASTA format):
I only want to see sequences that are mapped (all populations).     (see an example)

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