Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. It implements different reduced AA alphabets to group AAs of similar properties. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. The significance level was set at 0.05 for all tests. For yeast NatA substrate specificity analyses, the same set of subsequences of 25 residues from the N-termini of the 285 NatA substrates was used as the input set, while background models for Fisher’s exact test and Z-test were built from all subsequences and from randomly sampled subsequences of 25 AA residues from the N-termini of the yeast proteins not including the 285 NatA substrates, respectively. For human GRB substrate specificity analyses, the same set of 416, equal-length subsequences of 30 residues centered on the cleavage sites was used as the input set, while background models for Fisher’s exact test and Z-test were built from all subsequences and from randomly sampled subsequences of 30 AA residues from the UniProt human reference proteome, respectively. Fisher’s exact test ( A and C) and Z-test ( B and D) were performed to identify substrate sequence preferences of human GRB and yeast NatA, with a significance level of 0.05. S3 Fig: dagLogos resulting from different statistical test methods.
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