Protein BLAST: search protein databases using a protein query

BLASTP programs search protein databases using a protein query. more...

Enter Query Sequence

Enter accession number(s), gi(s), or FASTA sequence(s) [?] Clear

Query subrange [?]

Query subrangeFrom
Query subrangeTo

Or, upload file

[?]

Genetic code

Job Title

Enter a descriptive title for your BLAST search [?]

Align two or more sequences [?]

Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your sequences.
To get the CDS annotation in the output, use only the NCBI accession or gi number for either the query or subject. Reformat the results and check 'CDS feature' to display that annotation.

BLAST results will be displayed in a new format by defaultNew

You can always switch back to the Traditional Results page.

Enter Subject Sequence

Enter accession number(s), gi(s), or FASTA sequence(s) [?] Clear

Subject subrange [?]

Subject subrangeFrom
Subject subrangeTo

Or, upload file

[?]

Choose Search Set

Database

♦Database sequences non-default value [?]

Organism
Optional

exclude

Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown. [?]

Exclude
Optional

Exclude Models (XM/XP) Non-redundant RefSeq proteins (WP) Exclude Uncultured/environmental sample sequences

Program Selection Optimize for

Optimize for Highly similar sequences (megablast)

Optimize for More dissimilar sequences (discontiguous megablast)

Optimize for Somewhat similar sequences (blastn)

Choose a BLAST algorithm [?]

Megablast is intended for comparing a query to closely related sequences and works best if the target percent identity is 95% or more but is very fast.
Discontiguous megablast uses an initial seed that ignores some bases (allowing mismatches) and is intended for cross-species comparisons.
BlastN is slow, but allows a word-size down to seven bases.

more...

Algorithm

Algorithm Quick BLASTP (Accelerated protein-protein BLAST)

Algorithm blastp (protein-protein BLAST)

Algorithm PSI-BLAST (Position-Specific Iterated BLAST)

Algorithm PHI-BLAST (Pattern Hit Initiated BLAST)

Algorithm DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST)

Choose a BLAST algorithm [?]

QuickBLASTP is an accelerated version of BLASTP that is very fast and works best if the target percent identity is 50% or more.
BlastP simply compares a protein query to a protein database.
PSI-BLAST allows the user to build a PSSM (position-specific scoring matrix) using the results of the first BlastP run.
PHI-BLAST performs the search but limits alignments to those that match a pattern in the query.
DELTA-BLAST constructs a PSSM using the results of a Conserved Domain Database search and searches a sequence database.

Search database nr using Blastp (protein-protein BLAST)
Show results in a new window

Algorithm parameters

General Parameters Max target sequences

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

Short queries

Automatically adjust parameters for short input sequences [?]

Expect threshold

♦Expect threshold non-default value [?]

Word size

♦Word size non-default value [?]

Max matches in a query range

♦Max matches in a query range non-default value [?]

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