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MMseqs2

Status: checked baseline 18-8cc5c.

MMseqs2 provides fast sequence and profile search for large public protein sets. It can extend candidate discovery beyond a single BLAST pass while retaining tabular evidence for review.

Minimal pattern

mmseqs createdb <QUERY_FASTA> <QUERY_DB>
mmseqs createdb <TARGET_FASTA> <TARGET_DB>
mmseqs search <QUERY_DB> <TARGET_DB> <RESULT_DB> <TMP_DIR>
mmseqs convertalis <QUERY_DB> <TARGET_DB> <RESULT_DB> <OUTPUT_TSV>

Set sensitivity, coverage, identity, and target limits explicitly for the campaign.

Output contract

Record input accessions and hashes, MMseqs2 version, database build commands, search parameters, output schema, tabular results, and hashes. Keep large indexes in ignored runtime or external storage.

A sequence hit supports homology, not a specific enzyme function or physical cluster, without independent evidence.

Source: MMseqs2 releases.