The spectra of the four spots for each isolate were imported into BioTyper™ version 2.0 software (Bruker Daltonik GmbH) and analysed by standard pattern matching (with default parameter settings) against the spectra of 2,881 species used as references in the BioTyper™ database (these spectra are an integrated part of the BioTyper™ software version, as updated in June 2008).
We then used MSATCOMMANDER [ 12] and Phobos [ 20] to identify di-, tetra-,etra-, and penta-nucleotide repeat patterns with their default settings.
As can be seen from the diagram, similarly distributed proportions of different unit lengths of SSR patterns occur for all species and the most amounts of perfect and imperfect SSR repeats is the dinucleotide patterns with the default parameter settings of minimum length of 10 base pairs and noise rate of 20%.
They were derived using the pattern-search tool MEME (17) with default parameters of fingerprint width of 10 residues and minimum occurrence of one pattern per sequence.
The networks were scanned for 3-vertex topological patterns using the FANMOD software with default settings [ 27, 28].
Correlations between genes were derived from PCA of gene expression patterns using the prcomp function with default settings in the R package stats.
The signature was verified at ScanProsite [ 33] against all the three available databases (Swiss-Prot, TrEMBL and PDB Databases), with default settings for pattern options.
POCO was run with default settings, except for the pattern length selected as 5 bp.
Next, the MEME motif discovery tool (http://meme-suite.org/) was applied, with default parameter settings, to identify a DNA sequence pattern within the data [ 85].
Some banks, however, may flirt with default.
