blastp
Protein-to-protein sequence alignment search
TLDR
Align sequences using blastp with e-value threshold
$ blastp -query [query.fa] -subject [subject.fa] -evalue [1e-9]
Align sequences using blastp-fast$ blastp -task blastp-fast -query [query.fa] -subject [subject.fa]
Align with custom tabular 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 with multiple threads$ blastp -query [query.fa] -db [blast_database_name] -num_threads [16] -max_target_seqs [10]
Search the remote non-redundant protein database$ blastp -query [query.fa] -db nr -remote
SYNOPSIS
blastp [options]
DESCRIPTION
blastp performs protein-to-protein BLAST (Basic Local Alignment Search Tool) searches. It compares amino acid sequences to find regions of similarity, which can reveal functional, structural, or evolutionary relationships.
The tool is essential for identifying protein families, finding homologs across species, and annotating newly sequenced proteins based on similarity to known sequences.
PARAMETERS
-query file
Input file with query sequences in FASTA format-subject file
Subject sequence file for direct comparison-db name
BLAST database name for searching-evalue threshold
Expectation value (E) threshold for reporting matches-task name
Algorithm variant: blastp or blastp-fast-outfmt format
Output format (0=pairwise, 6=tabular, 7=tabular with headers)-out file
Output file name-num_threads n
Number of CPU threads to use-max_target_seqs n
Maximum number of aligned sequences to keep-remote
Execute search on NCBI servers
CAVEATS
Large database searches require significant memory and time. Remote searches are rate-limited by NCBI. Results should be interpreted in the context of sequence length and database size.
SEE ALSO
blastn(1), blastx(1), makeblastdb(1)