RaacLogo: a new sequence logo generator by using reduced amino acid clusters

Sequence logos give a fast and concise display in visualizing consensus sequence. Protein exhibits greater complexity and diversity than DNA, which usually affects the graphical representation of the logo. Reduced amino acids perform powerful ability for simplifying complexity of sequence alignment, which motivated us to establish RaacLogo. As a new sequence logo generator by using reduced amino acid alphabets, RaacLogo can easily generate many different simplified logos tailored to users by selecting various reduced amino acid alphabets that consisted of more than 40 clustering algorithms. This current web server provides 74 types of reduced amino acid alphabet, which were manually extracted to generate 673 reduced amino acid clusters (RAAC5) for dealing with protein alignment. A two-dimensional selector was proposed for easily selecting desired RAAC5 with underlying biology knowledge. It is anticipated that the RaacLogo web server will play more high-potential roles for protein sequence alignment, topological estimation and protein design experiments. RaacLogo is freely available at http://bioinfor.imu.edu.cn/raaclogo.

Automated summary

RaacLogo is a new sequence logo generator that can easily generate customized simplified logos for users by using reduced amino acid alphabets. The website provides 74 types of reduced amino acid alphabets, and a two-dimensional selector is proposed for easily selecting desired reduced amino acid clusters. It is anticipated that RaacLogo web server will play a more high-potential roles in protein sequence alignment, topological estimation and protein design experiments.