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blastp — Protein-Protein BLAST. More information: <https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendi

Submitted by: @import:tldr-pages·Mar 2, 2026·

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linux

Problem

How to use the blastp command: Protein-Protein BLAST. More information: <https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastp_application_options/>.

Solution

blastp — Protein-Protein BLAST. More information: <https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastp_application_options/>.

Align two or more sequences using blastp, with the e-value threshold of 1e-9, pairwise output format, output to screen:

blastp -query {{query.fa}} -subject {{subject.fa}} -evalue {{1e-9}}

Align two or more sequences using blastp-fast:

blastp -task blastp-fast -query {{query.fa}} -subject {{subject.fa}}

Align two or more sequences, custom tabular output format, output to file:

blastp -query {{query.fa}} -subject {{subject.fa}} -outfmt '{{6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident}}' -out {{output.tsv}}

Search protein databases using a protein query, 16 threads to use in the BLAST search, with a maximum number of 10 aligned sequences to keep:

blastp -query {{query.fa}} -db {{blast_database_name}} -num_threads {{16}} -max_target_seqs {{10}}

Search the remote non-redundant protein database using a protein query:

blastp -query {{query.fa}} -db {{nr}} -remote

Display help (use -help for detailed help):

blastp -h

Code Snippets

Align two or more sequences using blastp, with the e-value threshold of 1e-9, pairwise output format, output to screen

blastp -query {{query.fa}} -subject {{subject.fa}} -evalue {{1e-9}}

Align two or more sequences using blastp-fast

blastp -task blastp-fast -query {{query.fa}} -subject {{subject.fa}}

Align two or more sequences, custom tabular output format, output to file

blastp -query {{query.fa}} -subject {{subject.fa}} -outfmt '{{6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident}}' -out {{output.tsv}}

Search protein databases using a protein query, 16 threads to use in the BLAST search, with a maximum number of 10 aligned sequences to keep

blastp -query {{query.fa}} -db {{blast_database_name}} -num_threads {{16}} -max_target_seqs {{10}}

Search the remote non-redundant protein database using a protein query

blastp -query {{query.fa}} -db {{nr}} -remote

Context

tldr-pages: linux/blastp

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