MaizeGDB BLAST

Please use the NCBI BLAST tool to BLAST against GenBank targets.
BLAST up to 5 sequences of up to 35,000 bp total length against maize datasets.

Other BLAST pages: Gramene.org, PlantGDB, NCBI,

right arrow Step 1: input your sequences (Raw sequence, FASTA, or Genbank accessions) question mark

Query sequence may be entered as FASTA (see the NCBI specification) or as raw sequence, or as a list of Genbank accessions or GI numbers. POPcorn will accept up to 5 input queries with a combined length of no more than 35,000bp. Some web services we connect to may reject queries of this maximum size. If that happens the results page will show an error for that target host/data set.

Be sure to indicate whether the sequence is nucleotides or amino acids, even if your input is Genbank ids.

Sequence in a format other than raw or FASTA will be rejected, as will sequence containing invalid characters (e.g. numbers). Extra spaces and blank lines are accepted.

Sequence may be either pasted into the text box given or uploaded from a file.

NOTE: if the input contains more than one sequence, the sequence must be all nucleotide or all amino acids.

Sequence type: Nucleotides Amino Acids
Enter your sequence: (example)

or upload from file:
right arrow Step 2: select datasets question mark
Select one or more BLAST targets to search by typing all or part of its name into the second BLAST target box. You can restrict the list of BLAST targets by typing all or part of a cultivar name into the first filter box.

Selected targets will appear in a list below the BLAST target box. You can see descriptions of your selected targets by moving your mouse over their names.

You can remove a selected dataset by clicking its "remove" button.

Include: genomes gene models both
Close X
Description of selected dataset goes here.
right arrow Step 3: select BLAST parameters question mark
Select BLAST parameters by choosing one of the preset options or by modifying the advanced settings. Click the expand button to see the advanced settings. Move your mouse over the radio button text to see a description.
Optimize for: High similarity Low similarity Short sequences

expand image advanced settings
right arrow Step 4: select output type question mark
Choose the output format. Move your mouse over the radio button text to see a description.
Enhanced output BLAST table output BLAST text output
Name your sequence (optional) BLAST >>
E-mail (optional)

Citation: Cannon et al., 2011 "POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data"

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Overview of BLAST

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing similarity in biological sequences. It operates on such sequences as the sequence of amino acids in proteins or the sequence of nucleotides of DNA or RNA molecules.

Learn more about BLAST here.

The BLAST home page is here.