Screenshots of the P-POD web interface.

<p>(A) A portion of the results page for the <i>DPM1</i> OrthoMCL family is shown superimposed on the search form. Results from OrthoMCL are provided, and a link to the larger Jaccard family (B) is also available. Disease information from OMIM is displayed, as well as any relevant disease or cross-complementation literature.</p

Steps in the analysis pipeline.

<p>Steps in the analysis pipeline.</p

Number of proteins in each organism found in OrthoMCL or Jaccard families.

<p>Number of proteins in each organism found in OrthoMCL or Jaccard families.</p

OrthoMCL family of the alpha tubulins.

<p>This OrthoMCL family contains only the alpha tubulins, while the tubulin family generated by the Jaccard family (too large to be shown here) contains the alpha, beta, and gamma tubulins.</p

Functional conservation vs. ortholog prediction: comparing experimental results with the OrthoMCL ortholog predictions for disease-related families.

<p>In all but one of these experiments, the yeast gene was mutated and the gene from the other organism was tested for the ability to complement the mutant phenotype. In the one exception, the yeast gene <i>DPM1</i> was expressed in mouse. In the OrthoMCL column, “Yes” indicates that the OrthoMCL algorithm placed the two proteins in the same ortholog family, while “No” indicates it did not. In the Experimental column, “Yes” indicates functional complementation, while “No” indicates none. Thus, when both columns are the same, the OrthoMCL prediction is consistent with the experimental result i.e. in the cases where both are “Yes,” the predicted orthologs are functionally conserved, and when both are “No,” the proteins are not predicted to be orthologs, and they are not functionally conserved.</p

Sources and numbers of sequences analyzed.

<p>Sources and numbers of sequences analyzed.</p

The <i>MET3/MET14</i> families.

<p>(A) <i>MET14</i> Jaccard family, and (B) <i>MET3/MET14</i> OrthoMCL family.</p

Components of the analysis pipeline.

<p>Components of the analysis pipeline.</p

OrthoMCL and Jaccard clustering results for the second largest RNA polymerase subunit families of <i>S. cerevisiae.</i>

<p>The second largest subunits of RNA polymerase I, II, and III in yeast are named <i>RPA135, RPB2</i>, and <i>RET1</i>, respectively. (A) Phylogenetic tree display of OrthoMCL results showing individual yeast subunit <i>RPA135</i> and its predicted orthologs resolved into a distinct family. OrthoMCL results showing yeast RNA polymerase subunits <i>RET1</i> (B) and <i>RPB2</i> (C) resolved into separate families of orthologs. (D) Jaccard clustering results showing a “super family” of related RNA polymerase subfamilies. Arrows from each OrthoMCL family on the left point to the separate subfamilies in the Jaccard results. I to IV on the right of each tree indicates RNA polymerase subfamily. The second largest subunits for a fourth RNA polymerase, Pol IV, unique to plants were resolved into their own distinct two-member family by the OrthoMCL program (not shown), and were appropriately clustered with this superfamily by the Jaccard clustering method. (Adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000766#pone-0000766-g002" target="_blank">figure 2</a> of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000766#pone.0000766-Herr1" target="_blank">[15]</a>)</p