For all datasets, a small percentage of reads had at least one high-quality hit (Supplementary Table S3), an expected phenomenon related to the incompleteness of the information contained in the database of reference (Huson et al., 2007).
Moreover, with every new sample passing through the analysis, the database of reference SSR profiles is enlarged and the probability of identifying the closest relative or exactly matching accession is enhanced.
The absence of Halothermothrix was expected because this genus contains only the species present in M1, which were removed from the database of reference, as explained in Subsection 3.2.
For our purposes, the database of reference profiles was created from the above AtGenExpress dataset specific to UV-B, heat, salt, cold, osmotic, and drought treatments at the four initial time-points already detailed above.
Instead of assigning taxonomy based on a range of matches to sequences from a set of reference genomes, SPANNER considers the similarity of the overall LCA Profile of a sequence to a reference database of LCA Profiles similarly constructed from the database of reference genomes.
In summary, eligible patients were aged >16 years who had bacterial meningitis confirmed by culture of cerebrospinal fluid (CSF) and were listed in the database of the Netherlands Reference Laboratory for Bacterial Meningitis from October 1998 to April 2002.
Those short reads that passed quality control filtering were first aligned to the database of human reference genome sequences (hg19, GRCh37; http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/).ucsc.edu/goldenPath/hg19/bigZips/
Searches were done using the PubMed database, accessing the MEDLINE database of references and abstracts.
To explore the knowledge base of the field, a database of references in scholarly surveys of various aspects of innovation, published in "handbooks", is assembled and a new methodology for analysing the knowledge base of a field with the help of such data is developed.
The first step was to apply the search expressions in each database of references and save the returned results.
