Software and resources for alternative splicing: vast-tools, VastDB and Matt

Software and resources for alternative splicing: vast-tools, VastDB and Matt

Lab members: André Gohr, Yamile Marquez, Fede Mantica.
Funding: ERC Starting Grant, MINECO, CRG 

Another 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: 

(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 human, mouse, chicken, zebrafish, amphioxus, sea urchin, centipede, fruitfly, planarians and sea anemone, and we are constantly adding new species. Availability: https://github.com/vastgroup/vast-tools.

(ii) VastDB: Vertebrate Alternative Splicing and Transcription Data Base provides genome-wide alternative splicing and gene expression profiles for more than fifty cell and tissue types and developmental stages for human, mouse and chicken, obtained from hundreds of independent experiments profiled using vast-tools. The combination of both 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 and automatic primer design for validation. We are preparing a major update, with many new species. Availability: http://vastdb.crg.eu.

(iii) Matt: Matt 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: http://matt.crg.eu.

(iv) Other software: we are also developing new tools, including one to elucidate the order of intron removal and another one to assess exon orthology across any evolutionary scale.

 

Related publications:

  • 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., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B. J., Irimia, M. (2017). An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Research, 27(10), 1759–1768.
  • Irimia, M., Weatheritt, R.J., Ellis, J., Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O'Hanlon, D., Barrios-Rodiles, M., Sternberg, M.J.E., Cordes, S.P., Roth, F.P., Wrana, J.L., Geschwind, D.H., Blencowe, B.B. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell, 159:1511-23.
  • Braunschweig, U., Barbosa-Morais, N.L., Pan, Q., Nachman, E., Alipahani, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., Blencowe, B.J. (2014). Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 24:1774-86.