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 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

Additional file 1: of Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation

Contains Figures S1–S9 and Tables S1–S11. (PDF 3906 kb

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 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-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