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