ASES: visualizing evolutionary conservation of alternative splicing in proteins

Diego Javier Zea; Hugues Richard; Elodie Laine

doi:10.1093/bioinformatics/btac105

ASES: visualizing evolutionary conservation of alternative splicing in proteins

Bioinformatics. 2022 Apr 28;38(9):2615-2616. doi: 10.1093/bioinformatics/btac105.

Authors

Diego Javier Zea¹, Hugues Richard², Elodie Laine¹

Affiliations

¹ Laboratoire de Biologie Computationnelle et Quantitative (LCQB), CNRS, IBPS, Sorbonne Université, 75005 Paris, France.
² Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.

PMID: 35188186
DOI: 10.1093/bioinformatics/btac105

Abstract

Summary: ASES is a versatile tool for assessing the impact of alternative splicing (AS), initiation and termination of transcription on protein diversity in evolution. It identifies exon and transcript orthogroups from a set of input genes/species for comparative transcriptomics analyses. It computes an evolutionary splicing graph, where the nodes are exon orthogroups, allowing for a direct evaluation of AS conservation. It also reconstructs a transcripts' phylogenetic forest to date the appearance of specific transcripts and explore the events that have shaped them. ASES web server features a highly interactive interface enabling the synchronous selection of events, exons or transcripts in the different outputs, and the visualization and retrieval of the corresponding amino acid sequences, for subsequent 3D structure prediction.

Availability and implementation: http://www.lcqb.upmc.fr/Ases.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing*
Exons
Phylogeny
Proteins* / chemistry
RNA Splicing

Substances

Proteins