9.1 Introduction

As mentioned in the HitKeeper Manual [2], a hit is where a match by a motif is located on a sequence, and consists of ’from’ and ’to’ coordinates. Yet, an arrangement of motifs along a sequence is often more characteristic than the presence of any single motif1. Searching for such characteristic arrangements can thus enhance the selectivity of searches without lowering their sensitivity. An expression that specifies such a particular arrangement of motifs is called a metamotif, and a hit by a metamotif on a sequence also results in ’from’ and ’to’ coordinates. Metamotif queries are a logical extension of hit queries.

The operator mom_query (“motif of motif”) is designed for queries about such metamotifs. It is currently the most sophisticated operator of HitKeeper.

Note:

  • The argument metamotif=... is mandatory. The syntax is explained in the next chapter.
  • The usage of the options seq_source, seq_name, not_seq_name is identical to that in hit_query or seq_query.
  • The usage of the options mot_source, mot_name, signif only affects the wildcard operator (explained below; see section 10.8) used by the metamotif query.

 

9.2 Options

As an overview, the following constraints are supported:

metamotif=...
Refer to the mom_query documentation for the complete syntax.
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.
not_seq_name=...
A list of sequence entry names to be excluded from the results (logical NOT to restrict the two previous constraints).
mot_source=...
Scope of the ? operator:
mot_name=...
Scope of the ? operator: A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results.
not_mot_name=...
Scope of the ? operator: A list of motif entry names to be excluded from the results (logical NOT to restrict the two previous constraints).
signif=...
Scope of the ? operator: A list of hit signif to be included in the results.
not_signif=...
Scope of the ? operator: A list of hit signif to be excluded from the results.
-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.

1For example, protein kinase domains occur in a large number of proteins; so do sterile alpha domains; but only ephrin receptors have a protein kinase domain followed by a sterile alpha.