Most of the systems assume that users could formulate their QoS requirements easily and accurately by using the provided query languages.
For instance, blue, uniform patches of images depicting the sky or sea could boost the retrieval performance of a system that is ranking landscape images to a provided query.
We have therefore provided querying capabilities using mySQL queries.
Annotation with EDAM denotes topics of the resources, types of data provided, query parameters and output formats.
Gene models provided query sequences to search the National Center for Biotechnology Information (NCBI) non-redundant protein database and the Arabidopsis thaliana protein database [ 46].
The built-in BLAST in HelicoBase provides two main functions: (1) standard BLAST which will search the provided query sequence against genome or ORF sequences (either nucleotide or protein) in HelicoBase; (2) VFDB BLAST which searches the provided query sequence against the Virulence Factor Database (VFDB) [ 43, 44, 52].
Looking this reference up, it seems that the obtained hits came from HHpred against Pfam-A with E-values rather borderline close to generally accepted significance thresholds depending on the provided query and length.
This means that users must make some decisions to provide queries, and this causes difficulties for reflecting their demands.
To provide queries on tops of huge amounts of data but also through, because there's an API, That you can now write to, to feed all of the systems, as well.
Like STAMP, MotIV provides queries to the JASPAR database [22], and users can flexibly input other sets of reference PWMs (e.g. TRANSFAC [23], UniProbe [24], DBTBS [25], or RegulonDB [26]).
None of the listed tools provide queries based on functional annotation or the integration of expression data.
