Matt: Unix tools for alternative splicing analysis

Bioinformatics
André Gohr, Manuel Irimia

Abstract

Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality. matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules/the R Base package simplifying its installation. Supplementary data are available at Bioinformatics online.

References

Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gene Yeo, Christopher B Burge
Oct 27, 2006·Nature·Jernej UleRobert B Darnell
Dec 3, 2010·PLoS Computational Biology·André CorveloEduardo Eyras
Jul 13, 2013·Nature·Debashish RayTimothy R Hughes
May 16, 2014·Nucleic Acids Research·Inbal PazYael Mandel-Gutfreund
May 14, 2016·Nucleic Acids Research·Juw Won ParkYi Xing

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Citations

Nov 23, 2018·Nature·Ferdinand MarlétazManuel Irimia
Mar 6, 2019·Nature Ecology & Evolution·Antonio Torres-MéndezManuel Irimia
Aug 22, 2021·Genome Biology·Yamile MárquezManuel Irimia
Jan 29, 2022·Science Advances·Antonio Torres-MéndezManuel Irimia

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