Exact(3)
The building blocks of the queries per database are specified in the Appendix.
Within the 'browse' and 'search result' table, the criteria for including the specific gene in the database are specified.
If all modifications in the Unimod [ 18] database are specified, all search engines would not work properly.
Similar(57)
No database is specified for HHpred searches (page 34, line 741).
In one case, a search tool is specified (PSI-BLAST), but the database(s) is not (page 34, line737); whereas in the other case a database is specified (CDD), but the search tool (RPS-BLAST) and its parameters are not (page 34, line 740).
In relational databases, finite domains are specified by a relational schema, which are typically not in place for real-life graphs.
Given a parent ion mass and a database, once the allowable PTMs are specified, the number of peptides along with possible types of modifications are fixed.
Recent initiatives specifically aim at solving this issue: for instance, textual annotations in UniProtKB/SwissProt are being progressively replaced by direct references to reactions from UniPathway, a metabolic database in which all reaction steps are specified up to the chemical level (see Table 1).
The automation actor are specified in terms of interfaces, database and functions.
Details on database searching, protein identification, and ion-current-based quantification are specified in the Supporting Information.
No amounts are specified.
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