Ranks of known TAL effector target sites.

<p>Ranks of known TAL effector target sites among the TALgetter predictions in independent cross validation-like experiments (TALgetter CV) and for the final version used in the web-application and command line program (TALgetter final).</p

Recognition of predicted target sites by AvrXa10.

<p>(A) RVDs of the TAL effector AvrXa10 and predicted target sites. The optimal box is deduced from the known RVD specificites, while box 6, box 38, box 41, and box 98 are TALgetter AvrXa10 target predictions from rice promoters. Mismatches and non-optimal RVD-base pair combinations are shaded in light and dark grey, respectively. (B) AvrXa10 and Hax3 target boxes are cloned upstream of the minimal <i>pBs4</i> promoter and a promoterless <i>uidA</i> reporter gene. The artificial TAL effector ArtBs4 targets the <i>pBs4</i> promoter and is used as control for reporter construct integrity. (C) Specific recognition of target boxes. Reporter constructs are codelivered via <i>A. tumefaciens</i> into <i>N. benthamiana</i> with (+) and without (−) constructs producing TAL effectors, respectively, and GUS reporter activity was determined two days post inoculation. Error bars indicate standard deviation ( samples). 4-MU, 4-methyl-umbelliferone. Leaf disks are stained with X-Gluc (5-bromo-4-chloro-3-indolyl--D-glucuronide). A blue color indicates reporter gene activity.</p

Data sets of putative target genes of expressed TAL effectors obtained from comparative studies (in alphabetical order).

<p>Data sets of putative target genes of expressed TAL effectors obtained from comparative studies (in alphabetical order).</p

<i>Oryza sativa</i> ssp <i>japonica</i> microarray experiments from PLEXdb used in this paper.

a<p><i>Xoo</i>: <i>X. oryzae</i> pv. <i>oryzae</i>; <i>Xoc</i>: <i>X. oryzae</i> pv. <i>oryzicola</i>.</p

Positional preference of TAL effector target sites relative to the TATA-box (left) and TC-box (right).

<p>The estimated density of positions from the positive set is plotted as a green line, while the density of the negatives is plotted in red. The green points at the bottom of the plots represent the distribution of positions from the positive set along the x-axis, where the points are distributed randomly in y-direction to make individual points distinguishable.</p

Comparison of TALgetter to Target Finder with a T (Target Finder T), or both T and C (Target Finder T/C) at position 0 on public gene expression data.

<p>We consider as performance measure the number of predicted targets that are supported by up-regulation according to gene expression data after <i>Xanthomonas</i> infection using a log fold-change of 1. Performance is measured for different rank cutoffs (Top 10, 20, 50, and 100 predictions) on the predictions for each TAL effector.</p

Predicted targets in <i>O. sativa</i>.

<p>List of predicted targets in <i>O. sativa</i>. For each predicted target, we list the name of the TAL effector, the locus ID and the description of the targeted gene, the rank among the predictions of TALgetter for the specific TAL effector, and the list of microarray experiments that support this target. The corresponding log-fold changes observed in the microarray experiments are given in parentheses. TAL effectors with a common target site are listed in the same row. If both TAL effectors have identical RVD sequences, they are separated by a slash. Otherwise, they are separated by an ampersand. Known target sites are marked with an asterisk.</p

Predicted targets in <i>C. sinensis</i>.

<p>List of predicted targets in <i>C. sinensis</i>. For each predicted target, we list the name of the TAL effector, the locus ID and the description of the targeted gene, the rank among the predictions of TALgetter for the specific TAL effector, and the corresponding log-fold change observed in the microarray experiment.</p

Overview of tools for predicting TAL effector (TALE) and TAL effector nuclease (TALEN) target sites.

a<p><a href="http://galaxy.informatik.uni-halle.de" target="_blank">http://galaxy.informatik.uni-halle.de</a>.</p>b<p><a href="https://tale-nt.cac.cornell.edu/node/add/talef-off" target="_blank">https://tale-nt.cac.cornell.edu/node/add/talef-off</a>.</p>c<p><a href="http://bioinfo-prod.mpl.ird.fr/xantho/tales/" target="_blank">http://bioinfo-prod.mpl.ird.fr/xantho/tales/</a>.</p>d<p><a href="http://bioinfo.mpl.ird.fr/cgi-bin/talvez/talvez.cgi" target="_blank">http://bioinfo.mpl.ird.fr/cgi-bin/talvez/talvez.cgi</a>.</p>e<p><a href="https://tale-nt.cac.cornell.edu/node/add/talef-off-paired" target="_blank">https://tale-nt.cac.cornell.edu/node/add/talef-off-paired</a>.</p>f<p><a href="http://idtale.kaust.edu.sa" target="_blank">http://idtale.kaust.edu.sa</a>.</p>g<p>only pre-defined data sets;</p>h<p>this manuscript;</p>i<p>GNU General public license;</p>j<p>Internet Systems Consortium license, only stand-alone application;</p

Positional preference of TAL effector target sites relative to the start codon (left) and the transcription start site (TSS, right).

<p>The estimated density of positions from the positive set is plotted as a green line, while the density of the negatives is plotted in red. The whiskers indicate the bandwith of the box kernel used to smooth the curves in a kernel density estimation. The green points at the bottom of the plots represent the distribution of positions from the positive set along the x-axis, where the points are distributed randomly in y-direction to make individual points distinguishable.</p