Descriptive statistics revealing genetic characteristics and variation of the ten microsatellite loci detected in the population of 55 <i>L. major</i> strains isolated from Tunisian rodents and worldwide.

<p>N, number of genotypes; NA, number of allele per locus; Ho, observed heterozygosity; He, expected heterozygosity; Fis, inbreeding coefficient.</p><p>Descriptive statistics revealing genetic characteristics and variation of the ten microsatellite loci detected in the population of 55 <i>L. major</i> strains isolated from Tunisian rodents and worldwide.</p

Theoretical sizes and repetition numbers among the ten-microsatellite loci in Tunisian studied isolates.

<p>*: New allele not previously described.</p><p>Theoretical sizes and repetition numbers among the ten-microsatellite loci in Tunisian studied isolates.</p

Geographical distribution of strains isolated from the Central Tunisia study area.

<p>Panel A shows the square delimited study area in the Governorate of Sidi Bouzid (in gray). Panel B represents the land satellite image of the study area showing the distribution of animal reservoir hosts from which the <i>L. major</i> strains were isolated. Isolates from <i>P. obesus</i> origin were noted P and colored in green, from <i>M. shawi</i> origin were noted Mer and colored in yellow, and from <i>M. nivalis</i> was noted M and colored in red. Spatial data related to the reservoir hosts of these strains were collected using the Global Positioning System (GPS). Satellite imagery: ArcGIS software.</p

Neighbour-joining tree inferred from the Dps distances calculated for 55 <i>L. major</i> strains isolated from different rodents (40 Tunisian and 15 from other geographic origins) according to the 10 microsatellites analyzed.

<p>Strains isolated among <i>P. obesus</i> (P), <i>M. shawi</i> (M), <i>Tatera sp.</i> (T) and <i>R. opimus</i> (R) were classified into 10 genotypes Lmj01, Lmj02, Lmj14, Lmj15, Lmj17, Lmj21, Lmj37, Lmj39, Lmj65 (as described in<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107043#pone.0107043-AlJawabreh1" target="_blank">[21]</a>) and RdTN from Africa (AF), Middle East (ME) and Central Asia (CA). RdTN indicates the genotype obtained from Tunisian reservoirs. Results are shown as radial tree where the percentages (under 80%) with which a branch is supported in 1000 bootstrap replications are indicated.</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

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

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