Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments

Abstract

Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge.

An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms

“…Quotients of category and ratio (efficiency) were used for cluster analysis and heat map preparation using fastcluster (D. Müllner, fastcluster: Fast hierarchical clustering routines for R and Python; http://math.stanford.edu/Bmuellner). For each sirtuin the 50 peptides with highest efficiency values (marked in Supplementary Data 1) were used as positive set to prepare Two Sample Logos 51 , with all other peptides as negative set. No significance was set to show all amino acids.…”

A systematic identification of species-specific protein succinylation sites using joint element features information

“…A sequence logo was then plotted for the seven examined species, aiming to identify the surrounding sequence motifs that distinguish the succinylated sites from the nonsuccinylated sites ( Figure 2). 34 Graphical sequence from two sample logos was used to generate the position-specific residue compositions within the multiple sequence alignments. The heights in the amino acid sequence logos were scaled according to their statistical significance test (Student's t-test by P,0.05).…”

Splice Site Recognition Using Lower Dimensional LHMM Features and SVM Classifier

“…This includes the last 9 bases of the exon and first 6 bases of the succeeding intron. The dataset is available at [28]. This data set is split into a training set and a testing set.…”

“…The test data set contains 208 true acceptor sites, 208 true donor sites, 881false acceptor sites, and 782 false donor sites. Figure 2 and 3 show the two sample logo [28] of NN269 acceptor and donor sites. They represent the residues enriched and depleted in the sample.…”