The sequence_db class: using sequence databases
Keywords: manual

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The `sequence_db` class: using sequence databases

The `sequence_db` class holds a database of sequences. Such a database is similar to a multiple sequence alignment, but contains less auxiliary information (for example, no sequence may contain gaps). This requires less memory than a true alignment, and is thus more suited for large databases of sequences. Such a database can be scanned for matches to an input sequence with sequence_db.search(), used to build sequence profiles with profile.build() or filtered by given criteria with sequence_db.filter().

Subsections

- sequence_db() -- create a new sequence database
- sequence_db.read() -- read a database of sequences
- sequence_db.write() -- write a database of sequences
- sequence_db.convert() -- convert a database to binary format
- sequence_db.search() -- search for similar sequences
- sequence_db.filter() -- cluster sequences by sequence-identity