Fig. 2: Motif analysis in Psph.
From: Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling
a Venn diagram comparing the 6mA motifs between WT and ΔhsdMSR. The LOST set is determined to exclusively contain the type 1 6mA motifs. b The number of modified bases covered in each tool in four sets, categorized based on their operational capabilities. The tools are classified into two main types: Single Mode and Comparison Mode. Single mode tools are designed to process one set of sequencing data at a time, whereas comparison mode tools can analyze and compare two different data sets simultaneously. Additionally, the tools are further divided based on the type of nucleotide predictions they offer. 6mA-specific Tools are specialized for predictions exclusively on adenine modifications, while All Bases Available Tools are equipped to provide predictions across all types of nucleotides. The data sets used in this analysis, namely WT, ∆hsdMSR, LOST, and WGA, are detailed in the “methods” section. c Motifs enrichment -log10(p value) and the number of enriched sites determined by MEME-Streme. The top 10,000 6mA sites called by each tool are included in this analysis. Dots hit zero if no corresponding motif are discovered. Fisher’s exact test was applied to calculate the p value. d Histogram displaying the example of 6mA sites in the ground truth and Tombo_levelcom results. e Summary of motif discovery results in WT, ∆hsdMSR, and LOST set.
