Biotech > FAQ > BLAST FAQ (Frequently Asked Questions)

Causes for "No significant similarity fo...

To see other biotech frequently asked questions, please visit

(Continued from previous question...)

Causes for "No significant similarity found"

Below are several reasons that a BLAST search can result in the "No significant similarity found" message.

Short Sequences: There is a special BLAST optimized for searching with small sequences. Go to the main BLAST web page and select the "Search for short nearly exact matches" link for Nucleotide - Nucleotide or Protein Protein sections.

Filtering: BLAST filters regions of low-complexity (for a description of low-complexity see "What is low-complexity sequence?" below). If your sequence contains large regions of "low complexity" it may not significant hits to the database. You can turn off filtering by setting the "Filter" option to "None" using the pull down tab.

Query Format: Another reason you may see the "No Significant Similarity found" message is using the wrong type of sequence in your search.

1) Accession/GI Number or FASTA. Check that you have the Input Data set to the correct format for your Query. Set the pull down menu to "Accession number or Gi" to search with GenBank accession numbers or Gi numbers. Set to FASTA for raw amino acid or nucleotide sequences. For more information on FASTA format, click here.

2) Sequence type and Program combination. You can search with an amino acid query sequence using the blastp and tblastn programs. With nucleotide query sequences you can use blastn, blastx, and tblastx. Please note that tblastx program cannot be used with the nr database on the BLAST Web page.

For more information on the BLAST programs, click here.

(Continued on next question...)

Other Frequently Asked Questions