Then, controllable probabilistic dependence would obtain if for some pairs' states λ, L-setting l, R-setting r and local physical quantities α and β, Pλ l r α β yr) ≠ Pλ l r β yr) obtained).
The default program settings were used in QuantiSNP for defining copy number states: EM-iters – the number of iterations used in training the model on the experimental data; L-setting – expected typical number of base pairs in a CNV-region (smoothing factor); and the maxcopy setting – maximal CN state value in the Markov model.
In this paper, we propose a new approximate algorithm, APMotif, which overcomes the local maximum drawback to some extent that is inherent in the EM motif-finding algorithms and guarantees that most motifs can be discovered for specific (l, d) settings.
Additional file 13 gives the evolutionary models, log-likelihood values (-ln L) and settings identified by Modeltest for the different datasets.
The other is associated with deep tight gas reservoirs, mainly universal reservoir densification (L), stable tectonic settings (W), widely distributed reservoirs (D), and source rocks in a close contact with reservoirs (S).
Cluster analysis was performed using "blastclust" (ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html) with the following settings, L 0.98 S 97, meaning that all the LTR 300 bp tracts sharing at least 97% similarity over at least 98% of their length were included in the same cluster.
The parameter settings l, m, W1 and W2 were chosen based on the filter frequency settings (see Montez et al. 2006).
The program was used with the following settings, L 0.51 S 80, meaning that all sequences sharing at least 80% similarity over at least 51% of their length were included in the same cluster.
Redundancy was removed with cd-hit at a level of maximal 90% sequence identity [ 20], the remaining sequences were aligned with MAFFT (using L-INS-I settings [ 21]) and the resulting multiple alignment was visualized and annotated in Jalview [ 22].
Additionally, a study by Stamminger and colleagues showed that the average water consumption for manual dishwashing increases if the load to be cleaned is divided into smaller portions, from on average 103 l for 12 place settings in one go, to more than 121 l six times for 2 place settings [6].
