SECISearch3和Seblastian：用于预测SECIS元件和硒蛋白的电子工具

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

作者信息

Mariotti Marco

机构信息

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

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

出版信息

Methods Mol Biol. 2018;1661:3-16. doi: 10.1007/978-1-4939-7258-6_1.

DOI:10.1007/978-1-4939-7258-6_1

PMID:28917033

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/ .

摘要

硒代蛋白基因的计算识别因UGA密码子具有终止密码子和硒代半胱氨酸的双重含义而变得复杂。硒代半胱氨酸插入序列（SECIS）元件是硒代半胱氨酸插入所必需的RNA结构，在许多生物信息学研究中已被用作硒代蛋白基因的标记。用于真核生物SECIS查找的最广泛使用的工具最近已升级到第三代，即SECISearch3。该程序也是Seblastian的一个组件，Seblastian是一个用于识别硒代蛋白基因的流程，它将SECIS查找作为第一步。本章构成了使用SECISearch3和Seblastian的实用指南，它们可以通过网页服务器http://seblastian.crg.eu / 或http://gladyshevlab.org/SelenoproteinPredictionServer/运行。