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Software and resources on alternative splicing: the VastDB framework

Software and resources on alternative splicing: the VastDB frameworkSoftware and resources on alternative splicing: the VastDB framework

Current lab members: Federica Mantica, Luis P. Iñiguez.
Former lab members: André Gohr, Yamile Marquez, Javier Tapial.
Funding: ERC Starting Grant, MCIN CRG.

A major task of our lab is to provide publicly available tools and resources to study alternative splicing and transcriptomics. We are currently developing and maintaining several tools, organized and developed around the VastDB framework. This framework is especially designed to aid biomedical researchers without a strong computational background. It offers tools and resources to: (i) quantify AS and identify differentially spliced AS events using RNA-seq data (vast-tools), (ii) perform multiple genomic and sequence analyses for investigating AS events (Matt), (iii) assess relative intron splicing order around exons of interest (Insplico), (iv) identify AS events with genomic and regulatory conservation among species (ExOrthist), and (v) help with the biological interpretation of the results, and, ultimately, with the identification of interesting AS events to design wet-lab experiments (VastDB and PastDB).
 


Summary of the VastDB framework (from Gohr, Mantica et al, 2022)
 
(i) vast-tools: Vertebrate Alternative Splicing and Transcription Tools is a toolset for profiling and comparing alternative splicing events and gene expression from RNA-Seq data. It is currently available for 20 species, and we are constantly adding new species. Availability: https://github.com/vastgroup/vast-tools.

(ii) Matt: it is a Linux command-line tool-kit for analyzing genomic sequences with focus on the downstream analysis of alternative splicing events. Being a POSIX-style command-line tool-kit, Matt is run on the terminal of any Linux-like system. Availability: https://gitlab.com/aghr/matt.

(iii) Insplico: it is the first standalone tool to quantify intron splicing order around exons of interest that works with both short and long read sequencing technologies. Availability: https://gitlab.com/aghr/insplico.

(iv) Exorthist: fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. Availability: https://github.com/biocorecrg/ExOrthist.

(v.a) VastDB: Vertebrate Alternative Splicing and Transcription Data Base provides genome-wide alternative splicing and gene expression profiles for dozens of cell and tissue types and developmental stages for (currently) human, mouse, rat, cow, chicken, zebrafish and fruitfly obtained from hundreds of independent experiments profiled using vast-tools. The combination of resources will allow the users to easily put their alternative splicing event of interest into a wide regulatory and evolutionary context. Furthermore, VastDB includes multiple features such as impact on protein sequence and domains, evolutionary conservation (through Exorthist) and automatic primer design for validation. Availability: http://vastdb.crg.eu.

(v.b) PastDB: Plant Alternative Splicing and Transcription Data Base. Sister of VastDB, this resource offers similar data for the plant model Arabidopsis thaliana.

Related publications:

  • Gohr, A., Torres-Mendez, A., Bonnal, S.†, Irimia, M.† (2022). Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads. bioRxiv. doi: 10.1101/2022.08.15.503947.
  • Gohr, A., Mantica, F., Hermoso-Pulido, A., Tapial, J., Márquez, Y., Irimia, M.† (2022). Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework. Methods Mol Biol. 2537:97-128.
  • Marquez, Y.†, Mantica, F., Cozzuto, L., Burguera, D., Hermoso-Pulido, A., Ponomarenko, J., Roy, S.W., Irimia, M.† (2021). ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Genome Biol, 22:239.
  • Martín, G.†, Márquez, Y., Mantica, F., Duque, P., Irimia, M.† (2021). Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Genome Biol, 22:35.
  • Gohr, A., Irimia, M. (2019). Matt: Unix tools for alternative splicing analysis. Bioinformatics, 35:130-132.
  • Tapial, J., Ha, K.C.H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayón, M., Manzanares, M., Ponomarenko, J., Blencowe, B.J.†, Irimia, M.† (2017). An Alternative Splicing Atlas Reveals New Regulatory Programs and Genes Simultaneously Expressing Multiple Major Isoforms in Vertebrates. Genome Res, 27:1759-1768.