5.1 Scope

The seq_query operation returns a list of seq names. It is designed for:

  • performing logical operations on lists of sequences
  • running full-text searches in the descriptions attached to every sequence.

 

5.2 Out of Scope

  • For querying and filtering sequences by taxonomy, use hat_query (section 11).
  • For querying sequences according to matches by motifs (“hits”), use hit_query (section 11) and mom_query (section 10).

 

5.3 Options

The following constraints can be used in any combination and order. Please keep in mind that the constraints must be satisfied independantly (they are joined with a logical AND): if one of those is not fulfilled, the query will return an empty result.

seq_source=...
A non-empty list of sequence database names.
seq_name=...
A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results.
and_seq_name=...
A list of sequence entry names to be included in the results (logical AND with the previous constraint).
not_seq_name=...
A list of sequence entry names to be excluded from the results (logical NOT to restrict the two previous constraints).
desc_text=...
A list of words to search for.
min_score=...
A positive real number.
prop_key=...
Limit the search to the sequence with the given property key(s).
prop_value=...
Limit the search to entries with the supplied property value(s). The exhaustive list of all entries matching the criteria is returned. This is a major distinction from the built-in synonymy mechanism that returns at most one sequence.
-lim=...
Maximum number of rows to be returned.
-ref=...
A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed.