For more information on using MMseqs2 please see Söding Lab - MMseqs2.
Publication: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Here are the MMseqs2 output headers typically included in the resulting tab-delimited files: Query Sequence ID: Identifier for the sequence being queried. Target Sequence ID: Identifier for the matching sequence in the database. Percentage Identity: Percentage of identical matches in the alignment. Alignment Length: Length of the alignment between the query and target. Number of Mismatches: Number of mismatches in the alignment. Number of Gap Openings: Number of gaps introduced in the alignment. Query Start: Start position of the alignment on the query sequence. Query End: End position of the alignment on the query sequence. Target Start: Start position of the alignment on the target sequence. Target End: End position of the alignment on the target sequence. E-value: Statistical significance of the alignment. Bit Score: Score assigned to the alignment based on similarity.