In practice, for TF clustering, the parameter of length coverage threshold (−L) was changed from 0.60 to 0.95, with 0.05 as the step size, and the parameter of identity percentage (−S) was changed from 60 to 95, with 5 as the step size.
We selected 1,785 contigs containing domains supposedly corresponding to TE sequences and clustered them using BLASTClust (ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html, last accessed September 1, 2014) with the following parameters: 90% of identity and 60% of coverage.
Repeated elements were then removed using RepeatMasker [ 44] with a Viridiplantae database compiled in RepBase (01/08/2008 version) [ 45] to which we added the Silene latifolia - specific repeated elements identified by Cermak and coworkers [ 32]. EST reads were then clustered and contigs built using TGICL [ 46] with the default parameters (95% of identity and 40 bp minimum for sequence overlap).
Furthermore GAAS was used to generate estimates of the community composition using parameters of 50% identity, 50% read coverage, minimum 10e−6 e-value, weighing all hits and normalizing for genome length.
First, CLOBB analyses were performed using parameters of 95% identity and 50 bp coverage (Table 1), resulting in 10,261 clusters (6,196 singletons and 4,065 contigs) (Fig. 2).
The common genome of the five strains was determined using the BlastClust algorithm [ 86] using minimum parameters of 90% identity and 80% length coverage for proteins to be included in the same cluster.
Earthquake magnitude is one of the most important parameters to identity the strong ground motion.
In BLASTp comparison parameters, the percentages of identity and e-value were kept <35% and 0.005, respectively.
With a less strict parameter of 90% of identity we mapped 86% of the reference transcripts in the 'Sultanina' assembly.
The threshold parameters of 32.5% identity with ClustalW and a BlastP E-value of 10−50, are different to those used previously, and were derived by optimizing pham assembly over a range of possible values (S.G.C., R.W.H., G.F.H., manuscript in preparation).
