GenOuest Bioinformatics Platform

Blast 2.2.28+

Program selection Program selection


PSI-BLAST, PHI-BLAST and DELTA-BLAST can be used to find distantly related sequences

Query sequence Query sequence


FASTA format. Length is limited to 20Mb

FASTA format. File size is limited to 20Mb

Databank selection Databank selection


File size is limited to 20Mb
Please wait while loading the databank list

General parameters General parameters


The statistical significance threshold for reporting matches. Lowest values are the most stringent.

The length of the seed that initiates an alignment.

The length of the seed that initiates an alignment.

The length of the seed that initiates an alignment.

The length of the seed that initiates an alignment.

Maximum number of aligned sequences to display

Scoring parameters Scoring parameters


First number is the reward when two aligned nucleotides match.
Second number is the penalty when two aligned nucleotides are different.

First number is the reward when two aligned nucleotides match.
Second number is the penalty when two aligned nucleotides are different.

Substitution matrix for scoring any pair of residues.
BLOSUM45 or PAM70 are for more divergent sequences. BLOSUM80 or PAM30 are for less divergent sequences.

Penalties when opening and extending a gap in each alignment.

Penalties when opening and extending a gap in each alignment.

Matrix adjustment method to compensate for amino acid composition of sequences.

Matrix adjustment method to compensate for amino acid composition of sequences.

Filters and masking Filters and masking


Mask off segments of the query sequence that have low compositional complexity.

Mask only when finding alignment seeds, not during extension.

Filter regions in lower case in query sequence.

PSI-BLAST and PHI-BLAST PSI-BLAST and PHI-BLAST


Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.

Set the statistical significance threshold to include a domain in the model used by DELTA-BLAST to create the PSSM .

Number of iterations

If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134).

Upload a Position Specific Score Matrix (PSSM) that you previously downloaded from a PSI-BLAST iteration. You may search a different database than that used to generate the PSSM, but you must use the same query.

Enter a PHI pattern (PROSITE format) to start the search. PHI-BLAST may perform better than simple pattern searching because it filters out false positives (pattern matches that are probably random and not indicative of homology).

Discontiguous Word Options Discontiguous Word Options


Total number of bases in a seed that ignores some positions.

Specifies which bases are ignored in scanning the database.
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