Which BLAST options should I change?

There are a number of options that can be configured when using BLAST search programs. Setting these options to relevant values can have a great impact on the search result. A few of the key settings are described briefly below.

The E-value

The expect value (E-value) describes the number of hits one can expect to see matching the query by chance when searching against a database of a given size. An E-value of 1 can be interpreted as meaning that in a search like the one just run, you could expect to see 1 match of the same score by chance once. That is, a match that is not homologous to the query sequence. When looking for very similar sequences in a database, it is often beneficial to use very low E-values.

E-values depend on the query sequence length and the database size. Short identical sequence may have a high E-value and may be regarded as "false positive" hits. This is often seen if one searches for short primer regions, small domain regions etc. Below are some comments on what one could infer from results with E-values in particular ranges.

Gap costs

For blastp it is possible to specify gap cost for the chosen substitution matrix. There is only a limited number of options for these parameters. The open gap cost is the price of introducing gaps in the alignment, and extension gap cost is the price of every extension past the initial opening gap. Increasing the gap costs will result in alignments with fewer gaps.


It is possible to set different filter options before running a BLAST search. Low-complexity regions have a very simple composition compared to the rest of the sequence and may result in problems during the BLAST search [Wootton and Federhen, 1993]. A low complexity region of a protein can for example look like this 'fftfflllsss', which in this case is a region as part of a signal peptide. In the output of the BLAST search, low-complexity regions will be marked in lowercase gray characters (default setting). The low complexity region cannot be thought of as a significant match; thus, disabling the low complexity filter is likely to generate more hits to sequences which are not truly related.

Word size

Changing the word size has a great impact on the seeded sequence space as described above. But one can change the word size to find sequence matches which would otherwise not be found using the default parameters. For instance the word size can be decreased when searching for primers or short nucleotides. For blastn a suitable setting would be to decrease the default word size of 11 to 7, increase the E-value significantly (1000) and turn off the complexity filtering.

For blastp a similar approach can be used. Decrease the word size to 2, increase the E-value and use a more stringent substitution matrix, e.g. a PAM30 matrix.

The BLAST search programs at the NCBI adjust settings automatically when short sequences are being used for searches, and there is a dedicated page, Primer-BLAST, for searching for primer sequences. https://blast.ncbi.nlm.nih.gov/Blast.cgi.

Substitution matrix

For protein BLAST searches, a default substitution matrix is provided. If you are looking at distantly related proteins, you should either choose a high-numbered PAM matrix or a low-numbered BLOSUM matrix. The default scoring matrix for blastp is BLOSUM62.