Advanced Sequence Search - BLAST

  • Updated
Download Icon Download


Automatically adjust parameters for short sequences

Check this box to automatically adjust parameters in BLAST for nucleotides that are short (such as hairpin and double-stranded RNA searches), which adjusts the word size (to 7), gap costs, match scores, and e-value. If selecting this option still results in getting too many answers or non-relevant answers, try using Motif search instead.


Expect value, the number of matches expected by chance; the value decreases as the score of the match increases; a lower e-value means a more stringent search.

Match/Mismatch Scores

Values assigned to identically matching bases (reward) and mismatching bases (penalty); select a higher reward/penalty ratio when searching more divergent sequences.

Query Coverage %

Minimum percentage of query that must match the subject; select 100% if the entire query should be present in sequence matches.

Word Size

Minimum size of match that starts a similarity search; a higher value means a more stringent search.

Gap Costs

In alignments, cost to open (Extension) and extend (Extension) a gap; increasing gap costs results in sequence matches with fewer gaps.

Sequence Identity %

Percentage match between the query and target sequences.

Low Complexity Filter?

The low complexity region (LCR) has unusual composition and this can create problems in sequence similarity searching.

These include homopolymeric runs, short-period repeats, and subtler over representation of one or a few residues.


The filter is used to mask common sequence parts in order to prevent BLAST® from reporting irrelevant hits because of significant similarity in these parts. Masked parts are given with a row of Xs in the protein alignment and Ns in nucleotide alignment.