search protein databases using a protein query (2025)

Note: Parameter values that differ from the default are highlighted in yellow and marked with ♦ sign

General Parameters Max target sequences

♦Max target sequences non-default value
Select the maximum number of aligned sequences to display Help

Maximum number of aligned sequences to display (the actual number of alignments may be greater than this).

Short queries

Automatically adjust parameters for short input sequences Help

Automatically adjust word size and other parameters to improve results for short queries.

Expect threshold

♦Expect threshold non-default value Help

Expected number of chance matches in a random model. more... Expect value tutorial

Word size

♦Word size non-default value Help

The length of the seed that initiates an alignment. more...

Max matches in a query range

♦Max matches in a query range non-default value Help

Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query. The algorithm is based upon //www.ncbi.nlm.nih.gov/pubmed/10890403

Scoring Parameters Matrix

♦Matrix non-default value Help

Assigns a score for aligning pairs of residues, and determines overall alignment score. more...

Match/Mismatch Scores

♦Match/Mismatch Scores non-default value Help

Reward and penalty for matching and mismatching bases. more...

Gap Costs

♦Gap Costs non-default value Help

Cost to create and extend a gap in an alignment. more...

Compositional adjustments

♦Compositional adjustments non-default value Help

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

Filters and Masking Filter

♦Low complexity regions filter non-default value Low complexity regions filter Help

Mask regions of low compositional complexity that may cause spurious or misleading results. more...

♦Species-specific repeats filter non-default value

Species-specific repeats filter for: Help

Mask repeat elements of the specified species that may lead to spurious or misleading results. more...

Mask

♦Mask for lookup table only non-default value Mask for lookup table only Help

Mask query while producing seeds used to scan database, but not for extensions. more...

♦Mask lower case letters non-default value Mask lower case letters Help

Mask any letters that were lower-case in the FASTA input. more...

Discontiguous Word Options Template length

♦Template length non-default value Help

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

Template type

♦Template type non-default value Help

Specifies which bases are ignored in scanning the database. more...

PSI/PHI/DELTA BLAST

PSSM ♦PSSM non-default value

PSSM is uploaded... Clear

Upload PSSM Optional

Help

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. more...

PSI-BLAST Threshold

Help

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

♦DELTA-BLAST Threshold non-default value Help

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

Pseudocount

♦Pseudocount non-default value Help

Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.

Search using Blastp (protein-protein BLAST)
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search protein databases using a protein query (2025)

References