Then, in each validation run, we take a test protein complex, identify a query disease as the one with which the complex is associated, pretend that all annotated associations between the query disease and proteins (or corresponding genes) are unknown, and then rank the test protein complex against a collection of control protein complexes.
Some studies reported music retrieval applications in which the target music is identified by a query music section [3, 4].
Eligible patients were first identified by a query of the QuadraMed health information system (QuadraMed Corporation Westonn, VA) as performed by the Jacobi Medical Center information technology (IT) department using a preexisting electronic decision support system.
Patients were identified through a query of an internal database which tracks respiratory viruses.
Motifs are identified in a query sequence in comparison to a family profile.
In a typical FASSM [ 9] run, motifs are identified in a query sequence in comparison to a set of family profiles.
The ligand/substrate specificities and/or reaction mechanisms that characterize these families are then used to predict the individual in vitro activities and the shared metabolic pathway identified by a query cluster.
For patients served through general medicine clinics at UCSF, approval was obtained to introduce the study with a letter from the principal investigator (PI) to prospective research subjects who had been identified through a query of patient medical record databases to have an ICD-9 code of depression and/or a medical history of taking antidepressant medication.
However a psi-blast search of the nr database with the n-terminal portion of a representative AC protein (Tb927.6.760) as a query identified a probable leucine/isoleucine/valine-binding protein precursor from the bacteria Bradyrhizobium japonicum (NP_773188.1 Psi-blast round 2 Evalue = 8×10−10) as a candidate homologue of the kinetoplastid AC family.
A BLASTX survey of GenBank, using the Oculina sequence as a query, identified a putative tachylectin from the larval transcriptome of the reef-building coral, Acropora millepora [GenBank: EZ038328][ 73].
