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Command: blastprotein

blastprotein  sequence  [ database  sequence-database ] [ version  1 | 2 | 3 ] [ matrix  similarity-matrix ] [ cutoff  evalue ] [ maxSeqs  M ] [ log  true | false ] [ name  N ] [ showResultsTable  true | false ] [ loadStructures  true | false ] [ showSequenceAlignment  true | false ] [ onlyBest  true | false ]

The blastprotein command runs a protein sequence similarity search using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). It is the command implementation of the Blast Protein tool. One use is to search with a target sequence of unknown structure to find templates for comparative modeling. See also: alphafold search, esmfold search

The query sequence can be given as any of the following:

The protein sequence-database to search can be:

The matrix option indicates which amino acid similarity-matrix to use for alignment scoring (uppercase or lowercase can be used):

The cutoff evalue is the maximum or least significant E-value needed to qualify as a hit (default 1e-3). Results can also be limited with the maxSeqs option (default 100); this is the maximum number of unique sequences to return; more hits than this number may be obtained because multiple structures or other sequence-database entries may have the same sequence.

The remaining options control what happens when the search completes:

UCSF Resource for Biocomputing, Visualization, and Informatics / April 2024