SequenceQuery
#
- class biotite.database.rcsb.SequenceQuery(sequence, scope, min_identity=0.0, max_expect_value=10000000.0)[source]#
Bases:
SingleQuery
A query for protein/DNA/RNA molecules with a sequence similar to a given input sequence using MMseqs2.
- Parameters:
- sequenceSequence or str
The input sequence. If sequence is a
NucleotideSequence
and the scope is'rna'
,'T'
is automatically replaced by'U'
.- scope{‘protein’, ‘dna’, ‘rna’}
The type of molecule to find.
- min_identityfloat, optional
A match is only returned, if the sequence identity between the match and the input sequence exceeds this value. Must be between 0 and 1. By default, the sequence identity is ignored.
- max_expect_valuefloat, optional
A match is only returned, if the expect value (E-value) does not exceed this value. By default, the value is effectively ignored.
Notes
MMseqs2 is run on the RCSB servers.
Examples
>>> sequence = "NLYIQWLKDGGPSSGRPPPS" >>> query = SequenceQuery(sequence, scope="protein", min_identity=0.8) >>> print(sorted(search(query))) ['1L2Y', '1RIJ', '2JOF', '2LDJ', '2LL5', '2MJ9', '3UC7', '3UC8']