You are likely a contributor to one of the 3.5 billion search queries the website processes daily.
Custom Perl scripts were written to query the Index Fungorum database (http://www.indexfungorum.org/), using the Index Fungorum Fungus API to query the website to return taxonomic information on the additional species, absent from the UNITE database.
Structured information on explicit PPIs extracted from MEDLINE and other sources is freely available in the STRING database [10], or can be found by querying the iHOP website [11].
In addition, we also queried the GEO website (http://www.ncbi.nlm.nih.gov/geo/) for "GPL96" and "GPL570" to obtain the annotation summary for each of the datasets.
The following search key terms were used to query the PubMed website: "inherited breast cancer," "breast cancer AND susceptibility," "breast cancer AND somatic alterations," "breast cancer AND epigenetic," "breast cancer AND miRNA".
Japanese HapMap genotyping data of the HOX9 SNPs were retrieved from the International HapMap Project website by querying the HapMap Data Release #28.
With several known amino acid sequences of the Rab gene family members, seed file (PF00071) about the Rab domain was queried on the website of Pfam data base.
We make note of these exceptional cases and users are alerted when these genes are queried on the website.
MutationTaster scores and predictions were also extracted from dbNSFP, which were originally queried from the website of MutationTaster.
However, we hope the simplicity of generating the MartService and Perl API queries via the website will encourage the novice user to use these interfaces where appropriate.
However, we found that a variety of orthologous TFs in these families formed monophyletic clades, which were strongly supported by their high bootstrap values (nearly 100% in several clades) of the constructed phylogenetic trees mentioned above (phylogenetic trees could be queried on the website).
