Hypsibius dujardini genome assembly

Genome sequence assembly of a single individual of Hypsibius dujardini Z151 sequencing reads (Illumina MiSeq 300bp paired end), using MaSuR-CA 3.1.3 software

Additional file 2: of MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data

Wide-range comparison of MCC values of MICOP, ARS, JTK, and LS for non-decaying data. Sampling interval and noise level were gradually adjusted. The bar indicates MCC values (1 indicates a perfect prediction, 0 indicates a random prediction, and − 1 indicates a prediction in complete disagreement). (PDF 75 kb

Factor scores for the first four principal components.

<p>The different colored lines are the natural separation of the results into the different simulation runs.</p

Comparison of RMSE scores in four models.

<p>Boxplot of the RMSE scores for four models, representing the similarities between simulated and natural GC skews in the four models (in 65 bacteria). The <i>p</i> values were calculated by a Wilcoxon test, * <i>p</i><0.05, ** <i>p</i><0.01.</p

Heat map of RMSE scores for probabilistic combination model.

<p>The conceptual scheme (A) and heat map of RMSE scores (B) for probabilistic combination of replication termination models. The x-axis represents the 65 organisms, and the y-axis represents the combination patterns. Each color represents one of the three models (blue = <i>dif</i>-stop model, yellow = fork-collision model and red = fork-trap model), and the width of colored regions represents their probability (B). The scales are logarithmic.</p

Examples of simulated GC skew.

<p>Examples of the overall shapes around the GC skew shift points (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034526#pone.0034526.s003" target="_blank">Figure S3</a> for comprehensive results from all organisms used in this work). The left figures show the overall GC skew graph, and close-ups of the regions around the shift point are shown to the right. In the right set of graphs, red, green, blue and purple lines show the natural GC skew, fork-trap model, fork-collision model and <i>dif</i>-stop model, respectively.</p

The original (template) network that gave rise to the data and the two best networks obtained from minimizing the error.

<p>Only the network connections were optimized in this case, with the kinetic parameters taking on the same values as those that generated the “data”. Both Optimized Network-1 (Figure 3(b)) and Optimized Network-2 (Figure 3(c)) had a value of 0 for the minimization function which was the RMSD of the model and the “data” values.</p

Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes-1

<p><b>Copyright information:</b></p><p>Taken from "Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes"</p><p>http://www.biomedcentral.com/1471-2148/7/128</p><p>BMC Evolutionary Biology 2007;7():128-128.</p><p>Published online 31 Jul 2007</p><p>PMCID:PMC1950709.</p><p></p>alignments of 49 species in the firmicutes. Numbers at the nodes represent posterior probabilities. The scale bar represents 0.1 substitutions per site. Letters A through G next to the species names represent the combinations of RNase H genes defined in Figure 1; B' indicates the presence of dsRHbd

The reactions taking place in our system

<p>The reactions taking place in our system</p

Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes-2

<p><b>Copyright information:</b></p><p>Taken from "Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes"</p><p>http://www.biomedcentral.com/1471-2148/7/128</p><p>BMC Evolutionary Biology 2007;7():128-128.</p><p>Published online 31 Jul 2007</p><p>PMCID:PMC1950709.</p><p></p> Additional File and were aligned by using the Clustal method. Arrows and rectangles indicate beta-strands and alpha-helices, respectively. The upper and lower secondary structures were generated on the basis of the RNase HI domains of [33] and [29]. Dark and light shadings indicate highly conserved and similar amino acid residues, respectively. Asterisks denote amino acid residues that are involved in the catalytic function of RNase HI. The boxed region below the label for alpha-helix 3 forms a basic protrusion handle in the RNase HI structure. The combinations of RNase H genes are represented to the right of the sequences (see the text for details). The symbols and indicate active and inactive RNase H, respectively