MaizeGDB BLAST
This is the beta version of the New and Improved BLAST feature. Please problems or any other feedback. The old BLAST utility is archived here, but will be shut down at the end of 2025.
Sequence type:
Enter your sequence below (example)
Queries are limited to 10 query sequences with combined size of 20000bp or less. 		OR enter a Genbank accession:

Select one or more target datasets
Species Assembly Target

Zm-B73-REFERENCE-NAM-5.0-Assembly X

Set BLAST parameters
Max target sequences Limit target sequences reported to this number.
E-value Maximum e-value. Set this to a value > 1 for short sequences. (more)
The e-value parameter does not so much filter the results as
change the behavior of the BLAST algorithms. For example, an
e-value of 1e-4 may miss a short sequence even if the
sequence finds a perfect match with an e-value of 0.

close
Word size The length of the initial exact match. A larger word size will generally speed up the search. Because different values are accepted for nucleotide vs protein BLAST searches, the word size selected here may be changed. (more)
Accepted values for each BLAST program. Default value is bold.

nucleotide - nucleotide (blastn) 7, 11
nucleotide - protein (blastx) 3, 6
protein - nucleotide (tblastn) 3, 6
protein - protein (blastp) 2, 3, 6

close
Percent identity cutoff A value between 0 and 100.
Max HSPs Maximum number of HSPs to report. 1 = report only the best HSP for each hit. Leave blank to report all HSPs.
Match/mismatch costs Reward/penalty values and gap costs.

Select output type