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SECISearch3 and Seblastian: In-Silico Tools to Predict SECIS Elements and Selenoproteins

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Selenoproteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1661))

Abstract

The computational identification of selenoprotein genes is complicated by the dual meaning of the UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used as markers for selenoprotein genes in many bioinformatics studies. The most widely used tool for eukaryotic SECIS finding has been recently improved to its third generation, SECISearch3. This program is also a component of Seblastian, a pipeline for the identification of selenoprotein genes that employs SECIS finding as the first step. This chapter constitutes a practical guide to use SECISearch3 and Seblastian, which can be run via webservers at http://seblastian.crg.eu/ or http://gladyshevlab.org/SelenoproteinPredictionServer/.

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Author information

Authors and Affiliations

  1. Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA

    Marco Mariotti

  2. Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain

    Marco Mariotti

  3. Universitat Pompeu Fabra (UPF), Barcelona, Spain

    Marco Mariotti

  4. Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain

    Marco Mariotti

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  1. Marco Mariotti
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Correspondence to Marco Mariotti .

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Editors and Affiliations

  1. Centre International de Recherche en Infectiologie, CIRI, Lyon, France

    Laurent Chavatte

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Mariotti, M. (2018). SECISearch3 and Seblastian: In-Silico Tools to Predict SECIS Elements and Selenoproteins. In: Chavatte, L. (eds) Selenoproteins. Methods in Molecular Biology, vol 1661. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7258-6_1

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  • DOI: https://doi.org/10.1007/978-1-4939-7258-6_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7257-9

  • Online ISBN: 978-1-4939-7258-6

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