Number of sequenced genomes and domain coverage in the Eukaryote tree.

<p>This figure reports the number of genomes entirely sequenced in each of the 5 supergroups of the Eukaryote tree <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095275#pone.0095275-Keeling1" target="_blank">[58]</a>. In each group, a few sequenced genomes are provided as example, along with statistics relative to Pfam domains (release 26): the proportion of proteins where at least one Pfam domain has been identified using recommended Pfam score thresholds (above), and the proportion of amino acids covered by a Pfam domain (below). Most of the genomes sequenced to date belong to the Unikont (241) and plant (60) super-groups. We can see that there is a marked difference in the protein domain coverage between these groups and the three other groups: while the proportion of proteins where at least one known Pfam domain is usually above 70% in Unikonts and plants, it lies between 50% and 60% in the other groups. Similarly, while the proportion of amino-acids covered by a Pfam domain is often above 40% in plants and Unikonts, it is around 22% in the other supergroups.</p

Sensitivity and accuracy of HHPRED+CODD and HMMER+CODD using the known Pfam domain occurrences for certifications.

<p>This figure reports the number of new domains (x-axis) certified by HHPRED+CODD (in orange and green for the phylum specific and non-specific approaches, respectively) and HMMER+CODD (blue) using local (left) and global (right) alignments for various FDR thresholds (y-axis).</p

New Pfam domains (release 26) identified at 5% and 10% FDR.

<p>The table reports the number of new domains identified by HHPRED (local mode, phylum non-specific approach) and CODD for the three certification types: known Pfam domains (Pfam), known InterPro non-Pfam domains (Interp), potential domains (Pot). “All”: results achieved when combining the 3 types. “# dom.”: number of new domains identified. “new fam.”: number of domain families that were not previously known in any protein of the organism. In each cell, the left and right numbers report the result at 5% and 10% FDR, respectively. Column “All”: The number in parenthesis reports the proportion of already known domains or family this represents. ^*For the certifications by Interpro domains, this is the number of domains identified at 12% FDR because no FDR below 10% can be achieved by this certification type.</p

New GO annotations at 5% FDR.

<p>“# known GO” is the number of known GO annotations from EuPathDB; “# GO known dom.” is the number of GO annotations that can be deduced from already known domains; “#GO new dom.” is the number of new GO annotations that can be deduced from new domains. Numbers in parenthesis report the number of annotations that confirm already known annotations or annotations deduced from known domains.</p

Sensitivity and accuracy of HHPRED and HMMER for <i>P. falciparum</i> and <i>L. major</i>.

<p>Number of new domains (x-axis) identified by HHPRED (green) and HMMER (blue) using local (left) and global (right) alignments for various FDRs (y-axis). For each approach, the two plain lines represent an upper and lower FDR estimate (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095275#s4" target="_blank">Methods</a> for details). Dashed lines represent the standard error associated with these two estimates. For the sake of clarity, only the standard error above (resp. below) the upper (resp. lower) FDR estimate are represented here.</p

Cross-validation experiments on <i>P. falciparum</i> and <i>L. major</i>.

<p>The test was done on the 561 and 913 proteins of <i>P. falciparum</i> and <i>L. major</i> that have at least two known Pfam domains, respectively. The table reports the number of domains identified by HMMER and HHPRED that are certified by CODD at 3% FDR. Columns “# total certif.” and “# recovered domains” reports the total number of certified domains and the number of discarded domains that are recovered, respectively. Column “# overlaps” reports the number of newly certified domains that overlap a discarded domain.</p

Virtual classroom using the Mconf web conferencing platform.

<p>Classrooms connected to the trainer and to other classrooms via the Mconf open-source web conferencing platform (<a href="http://mconf.org/" target="_blank">http://mconf.org</a>; in use here is the South African instance of Mconf <a href="https://mconf.sanren.ac.za/" target="_blank">https://mconf.sanren.ac.za/</a>, hosted by SANREN <a href="http://www.sanren.ac.za/south-african-nren/" target="_blank">http://www.sanren.ac.za/south-african-nren/</a>). Classrooms either activated their microphones or entered text into a chat box to ask questions to the trainer. Trainers activated their webcams while answering questions. Trainers were able to upload their session resources in the central panel of the Mconf interface should they have wanted to explain a concept on a particular lecture slide, for example. Note: Consent to publish this image was obtained from the trainer shown in the figure. Abbreviation: SANREN, South African National Research Network.</p

Location of classroom sites for 2016 iteration of the IBT course.

<p>Classrooms (20 classrooms across 10 African countries accommodating 364 participants in total) met each other virtually to widen the scope and improve the depth of biweekly contact sessions. Abbreviation: IBT, Introduction to Bioinformatics.</p

Pre-recorded lectures.

<p>Screenshot of a pre-recorded lecture with webcam activated. Note: Consent to publish this image was obtained from the individual in the figure.</p

Screenshots of Vula site for IBT_2016 course.

<p>(A) Landing page of course site showing all tools. (B) Forums tool specifically showing the number of people that read the response to a particular question. In this example, at the time that the screenshot was obtained, 14 people had read the question, and 12 people had read the answer. Please note: Consent to publish this screenshot was obtained from participants of the relevant discussion. Abbreviation: IBT, Introduction to Bioinformatics.</p