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Related Experiment Video

Updated: Mar 26, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

Roland F Schwarz¹, Asif U Tamuri², Marek Kultys³

¹European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK rfs@ebi.ac.uk.

Nucleic Acids Research

|January 29, 2016

Summary

This summary is machine-generated.

Alvis is a new platform for analyzing multiple sequence alignments (MSAs) and phylogenetic trees. It uses Sequence Bundles to visualize individual sequences and identify covariant sites, improving upon traditional Sequence Logos.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Sequence Logos are standard for visualizing multiple sequence alignments (MSAs) and motifs, but obscure individual sequences and covariant sites.
Sequence Bundles offer a one-to-one sequence representation, enabling visualization of covariant sites.

Purpose of the Study:

Introduce Alvis, an open-source platform for joint analysis of MSAs and phylogenetic trees.
Leverage Sequence Bundles for enhanced visualization and interactive exploration of sequence data.
Provide tools for detecting covariant sites, annotating phylogenetic trees, and performing numerical analyses.

Main Methods:

Developed Alvis, an open-source platform integrating MSAs and phylogenetic trees.
Employed Sequence Bundles as the primary visualization technique within Alvis.
Integrated interactive toolkits for covariant site detection, tree annotation, and motif discovery.

Main Results:

Alvis facilitates the detection of covariant sites and annotation of phylogenetic trees with evolutionary events (synapomorphies, homoplasies).
The platform supports motif detection and numerical analyses like dimension reduction and classification.
Alvis provides user-friendly, customizable, and publication-quality figure export.

Conclusions:

Alvis enhances the exploratory analysis of MSAs and phylogenetic trees through advanced visualization and interactive tools.
The platform, particularly its Sequence Bundles module, offers significant improvements over existing methods for sequence data analysis.
Alvis is accessible as a standalone application and a web-based module for broader usability.