Which BLAST options should I change?

The NCBI BLAST web pages and the BLAST command line tool offer a number of different options which can be changed in order to obtain the best possible result. Changing these parameters can have a great impact on the search result. It is not the scope of this document to comment on all of the options available but merely the options which can be changed with a direct impact on the search result.

The E-value

The expect value (E-value) can be changed in order to limit the number of hits to the most significant ones. The lower the E-value, the better the hit. The E-value is dependent on the length of the query sequence and the size of the database. For example, an alignment obtaining an E-value of 0.05 means that there is a 5 in 100 chance of occurring by chance alone.

E-values are very dependent 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. The default threshold for the E-value on the BLAST web page is 10. Increasing this value will most likely generate more hits. Below are some rules of thumb which can be used as a guide but should be considered with common sense.

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 the 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

Change of 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.

Fortunately, the optimal search options for finding short, nearly exact matches can already be found on the BLAST web pages http://www.ncbi.nlm.nih.gov/BLAST/.

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.