A new protein linear motif benchmark for multiple sequence alignment software-0

subset 1, showing the extreme observations (stars or circles), lower quartile, median, upper quartile, and largest observation in each similarity category. b) Execution times in seconds required to construct all the multiple alignments in Subset 1. Programs are displayed in the order of the Friedman test using the SPS scores for group V11 (additional file ), with the highest scoring program on the left.<p><b>Copyright information:</b></p><p>Taken from "A new protein linear motif benchmark for multiple sequence alignment software"</p><p>http://www.biomedcentral.com/1471-2105/9/213</p><p>BMC Bioinformatics 2008;9():213-213.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2374782.</p><p></p

A new protein linear motif benchmark for multiple sequence alignment software-4

subset 1, showing the extreme observations (stars or circles), lower quartile, median, upper quartile, and largest observation in each similarity category. b) Execution times in seconds required to construct all the multiple alignments in Subset 1. Programs are displayed in the order of the Friedman test using the SPS scores for group V11 (additional file ), with the highest scoring program on the left.<p><b>Copyright information:</b></p><p>Taken from "A new protein linear motif benchmark for multiple sequence alignment software"</p><p>http://www.biomedcentral.com/1471-2105/9/213</p><p>BMC Bioinformatics 2008;9():213-213.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2374782.</p><p></p

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences-3

query sequence are discarded. The distribution of the branch lengths appears more even in the recalculated phylogenetic tree (right). This refinement step improves the alignment quality. It also prevents artificially small sequence weights being obtained upon normalisation by the total branch length. The trees are calculated using the neighbor-joining procedure in ClustalW; they are then rooted using the query sequence as outgroup, as explained in the Sequence weights determination section.<p><b>Copyright information:</b></p><p>Taken from "A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences"</p><p>http://www.biomedcentral.com/1471-2105/9/229</p><p>BMC Bioinformatics 2008;9():229-229.</p><p>Published online 6 May 2008</p><p>PMCID:PMC2396637.</p><p></p

A new protein linear motif benchmark for multiple sequence alignment software-2

different conditions, showing the extreme observations (stars or circles), lower quartile, median, upper quartile, and largest observation. Significant differences, according to a Wilcoxon signed ranks test (p < 0.05), are indicated by an asterix on the x-axis. P-values for the Wilcoxon tests are available in additional file , table 3. a) SPS scores for alignments of sequences with validated motifs only compared to alignments including sequences with errors. b) SPS scores for alignments of sequences with validated motifs only compared to alignments including sequences containing false positive (FP) motifs. c) SPS scores for alignments of sequences with validated motifs only compared to alignments including sequences that do not contain any examples of the motif.<p><b>Copyright information:</b></p><p>Taken from "A new protein linear motif benchmark for multiple sequence alignment software"</p><p>http://www.biomedcentral.com/1471-2105/9/213</p><p>BMC Bioinformatics 2008;9():213-213.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2374782.</p><p></p

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences-2

. Dots in the upper right square correspond to well conserved instances that score highly with both models. Dots on the left half and above the diagonal, indicate poorly conserved instances that are scored higher by the EXC CONT model.<p><b>Copyright information:</b></p><p>Taken from "A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences"</p><p>http://www.biomedcentral.com/1471-2105/9/229</p><p>BMC Bioinformatics 2008;9():229-229.</p><p>Published online 6 May 2008</p><p>PMCID:PMC2396637.</p><p></p

Overview of Motifs Found in the Fly

<p>Significant predictions from the yeast two-hybrid set for the fly. Blue dots in the center of each cluster represent proteins with four or more interaction partners (red and white dots) containing at least one confidently predicted motif (<i>p-</i>value < 0.001; <i>S_cons</i> ≤ 8 × 10⁻¹⁵). Partner proteins containing the motif are represented by red dots, whereas proteins lacking the motif are indicated by white dots. Clusters are labelled as gene name→detected motif. Yellow circles enclose known motifs: SH3→PxxP [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-b38" target="_blank">38</a>], PP1→RVxF [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-b22" target="_blank">22</a>], C-terminal binding protein (CtBP)→PxDLS [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-b52" target="_blank">52</a>], SR splicing factors RS-rich segments [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-b53" target="_blank">53</a>], and CG6843→SxKSKxxK, a likely nuclear localization signal. The Translin→VxxxRxYS motif was experimentally tested (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-g003" target="_blank">Figure 3</a>). The grey circles enclose clusters with low-complexity patterns. Two additional known motifs were also found in the fly using more relaxed criteria than those used for the other motifs in the figure: Groucho→WRPW [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-b07" target="_blank">7</a>] and Dynein light chain→TQT [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-b26" target="_blank">26</a>] as the variant A(TI)QT(DE). The latter was also identified as significant in the domain sets. Proteins are denoted either by their FlyBase accession codes or protein names when available.</p

A Lit-1 MAP Kinase SxPxxxS Motif

<p>The MAP kinase lit-1 surrounded by its interaction partners containing the SxPxxxS motif. Details are as for <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030405#pbio-0030405-g003" target="_blank">Figure 3</a>. Yellow boxes show the location of deletion mutants known to affect the interaction. Cbr, <i>C. briggsae;</i> Cel, <i>C. elegans</i>.</p