Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data

Abstract

Summary: Current web-based sequence logo analyses for studying domain-peptide interactions are often conducted only on high affinity binders due to conservative data thresholding. We have developed Dynalogo, a combination of threshold varying tool and sequence logo generator written in the R statistical programming language, which allows on-the-fly visualization of binding specificity over a wide range of affinity interactions. Hence researchers can easily explore their dataset without the constraint of an arbitrary threshold. After importing quantitative data files, there are various data filtering and visualizing features available. Using a threshold control, users can easily track the dynamic change of enrichment and depletion of amino acid characters in the sequence logo panel. The built-in export function allows downloading filtered data and graphical outputs for further analyses. Dynalogo is optimized for analysis of modular domain-peptide binding experiments but the platform offers a broader application including quantitative proteomics.

Availability and implementation: Dynalogo application, user manual and sample data files are available at https://dynalogo.cam.uchc.edu. The source code is available at https://github.com/lafontaine-uchc/dynalogo.

Supplementary information: Supplementary data are available at Bioinformatics online.