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Introduction

MetaLogo is a tool for making sequence logos. A sequence logo is a graphical representation of the sequence conservation of nucleotides or amino acids (From wikipedia). For each site, the base (nucleotides or amino acids) frequencies or information contents (Thomas, 1986) are calculated. The higher the base, the more conservative it is.

There are several popular sequence logo making tools, such as WebLogo, Seq2Logo, LogoMaker, ggseqlogo and so on. However, most sequence logo tools were designed to highlight the conservations among sequences and to depress the variations. The more diverse the positions, the less signal indicated in sequence logos. This setting could help to reveal the real conserved motifs if the input sequences are indeed homologous. But when there exists intrinsic divergence among sequences, it is difficult for conventional sequence logo generators to sort out clues. Ortholog and paralog of sequences need to be considered when performing sequence analysis, especially for motif discovery. Among the sequenced data of natural DNA or amino acids, there may exist artificial synthesis and contaminated sequences, which also need to recognized when drawing sequence logos. Therefore, a reliable heterogeneity-aware sequence logo generator is needed.

To solve the problems, we developed MetaLogo, which take sequences with heterogeneity as input, then perform sequence clustering based on phylogenetic tree or user-defined grouping, and finally output sequence logos for each group and place them aligned in one figure. MetaLogo can highlight both the conserved motifs and diverse regions among groups, and related these homogeneities and heterogeneities to gene functions. Since the grouping are based on the phylogeny, MetaLogo could also be used to infer function or taxonomy of target sequences from its neighbor in the same group. Considering that MetaLogo does not assume that the input sequences are from one same homologous group, the motifs indicated by sequence logos from MetaLogo could be more informative and reliable than those from conventional sequence generators. To use homology information from outside the input sequences, users can use Consurf and MetaLogo together to get all the sequences of the homology group into MetaLogo to construct the sequence logo diagram of the evolution group.

MetaLogo provides several beautiful and useful layouts for multiple sequence logos, which gives people more choices for motif and pattern visualization. By developing convenient web sever, we also tried to help researchers who have no coding experiences to make satisfactory sequences logos.

Contents of MetaLogo tutorial

Install

Alignment

Python package

Webserver