Abstract
Sequence logos are a simple way to display a set of aligned sequences, and they are useful to identify conserved patterns. Since their introduction, several tools have been developed for generating these representations at the single residue level (amino acids or nucleotides). We have developed a tool to build sequence logos of protein-coding sequences at the codon level, allowing more accurate analysis of coding-sequences as they represent synonymous and non-synonymous changes instead of showing only changes that imply on amino acid substitutions. We built CoCoView on top of the Logomaker Python API. It creates codon sequence logos from a multiple sequence alignment of protein-coding sequences. Some properties of the data and the generated logos can be controlled by the end-users, such as data redundancy, plot type and alphabet color. • Split aligned sequences into codon positions; • For each position compute codon frequency and information content; • Use the computed information to plot the graphic.
Beatriz Rodrigues Estevam
Undergrad student - Biological Sciences (ESALQ/USP) - Plant genomics
I am very passionate about the ability to solve biological problems with bioinformatics.
Diego Mauricio Riaño-Pachón
Assistant Professor (MS3.2) in Computational, Evolutionary and Sistems Biology
I am a computational biologist/bioinformatician at the University of São Paulo, Campus Luiz de Queiroz (Piracicaba/SP, Brazil).