Blast server (v2.2.29+)

Job title

Email address

Program selection

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

Query sequence

Paste your sequence	FASTA format. Length is limited to 20Mb
Or select a file	FASTA format. File size is limited to 20Mb
Query genetic code

Databank selection

Databank type
Databank type
Select a personal databank (FASTA format)	File size is limited to 20Mb
Databank
Databank genetic code

General parameters

Expect	The statistical significance threshold for reporting matches. Lowest values are the most stringent.
Word size	The length of the seed that initiates an alignment.
Word size	The length of the seed that initiates an alignment.
Word size	The length of the seed that initiates an alignment.
Word size	The length of the seed that initiates an alignment.
Max target sequences	Maximum number of aligned sequences to display

Scoring parameters

Matrix	First number is the reward when two aligned nucleotides match. Second number is the penalty when two aligned nucleotides are different.
Matrix	First number is the reward when two aligned nucleotides match. Second number is the penalty when two aligned nucleotides are different.
Matrix	Substitution matrix for scoring any pair of residues. BLOSUM45 or PAM70 are for more divergent sequences. BLOSUM80 or PAM30 are for less divergent sequences.
Gap costs	Penalties when opening and extending a gap in each alignment.
Gap costs	Penalties when opening and extending a gap in each alignment.
Compositional adjustments	Matrix adjustment method to compensate for amino acid composition of sequences.
Compositional adjustments	Matrix adjustment method to compensate for amino acid composition of sequences.

Filters and masking

Low complexity regions	Mask off segments of the query sequence that have low compositional complexity.
Soft masking	Mask only when finding alignment seeds, not during extension.
Mask lower case letters	Filter regions in lower case in query sequence.

PSI-BLAST and PHI-BLAST

PSI-BLAST threshold	Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.
DELTA-BLAST threshold	Set the statistical significance threshold to include a domain in the model used by DELTA-BLAST to create the PSSM.
Iteration number	Number of iterations
Pseudocount	If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134).
Upload PSSM	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.
PHI-BLAST pattern	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

Template length	Total number of bases in a seed that ignores some positions.
Template type	Specifies which bases are ignored in scanning the database.