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