SECISearch3 and Seblastian: In-Silico Tools to Predict SECIS Elements and Selenoproteins.
作者： Marco Mariotti
DOI: 10.1007/978-1-4939-7258-6_1
关键词: Gene prediction 、 Computational biology 、 RNA 、 In silico 、 Selenocysteine incorporation 、 Gene 、 Computer science 、 Selenocysteine 、 Selenoprotein 、 Genomics
摘要: The computational identification of selenoprotein genes is complicated by the dual meaning UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used markers in many bioinformatics studies. most widely tool eukaryotic finding has recently improved to its third generation, SECISearch3. This program also a component Seblastian, pipeline that employs first step. chapter constitutes practical guide use SECISearch3 can be run via webservers at http://seblastian.crg.eu / or http://gladyshevlab.org/SelenoproteinPredictionServer/ .
springer.com
sci-hub.se 参考文章(45)
M.J. Berry, L. Banu, J.W. Harney, P.R. Larsen, Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. The EMBO Journal. ,vol. 12, pp. 3315- 3322 ,(1993) , 10.1002/J.1460-2075.1993.TB06001.X
I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster, Fast folding and comparison of RNA secondary structures Monatshefte Fur Chemie. ,vol. 125, pp. 167- 188 ,(1994) , 10.1007/BF00818163
Guy Slater, Ewan Birney, Automated generation of heuristics for biological sequence comparison BMC Bioinformatics. ,vol. 6, pp. 31- 31 ,(2005) , 10.1186/1471-2105-6-31
N Hubert, R Walczak, C Sturchler, E Myslinski, C Schuster, E Westhof, P Carbon, A Krol, RNAS MEDIATING COTRANSLATIONAL INSERTION OF SELENOCYSTEINE IN EUKARYOTIC SELENOPROTEINS Biochimie. ,vol. 78, pp. 590- 596 ,(1996) , 10.1016/S0300-9084(96)80005-8
S. Castellano, A. V. Lobanov, C. Chapple, S. V. Novoselov, M. Albrecht, D. Hua, A. Lescure, T. Lengauer, A. Krol, V. N. Gladyshev, R. Guigo, Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 16188- 16193 ,(2005) , 10.1073/PNAS.0505146102
Sergi Castellano, Nadya Morozova, Marta Morey, Marla J Berry, Florenci Serras, Montserrat Corominas, Roderic Guigó, In silico
identification of novel selenoproteins in the
Drosophila melanogaster
genome EMBO reports. ,vol. 2, pp. 697- 702 ,(2001) , 10.1093/EMBO-REPORTS/KVE151
Alexey V. Lobanov, Stephan Gromer, Gustavo Salinas, Vadim N. Gladyshev, Selenium metabolism in Trypanosoma: characterization of selenoproteomes and identification of a Kinetoplastida-specific selenoprotein Nucleic Acids Research. ,vol. 34, pp. 4012- 4024 ,(2006) , 10.1093/NAR/GKL541
M.T.A. da Silva, V.E.A. Caldas, F.C. Costa, D.A.M.M. Silvestre, O.H. Thiemann, Selenocysteine biosynthesis and insertion machinery in Naegleria gruberi Molecular and Biochemical Parasitology. ,vol. 188, pp. 87- 90 ,(2013) , 10.1016/J.MOLBIOPARA.2013.04.002
Sergey V. Novoselov, Deame Hua, Alexey V. Lobanov, Vadim N. Gladyshev, Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family. Biochemical Journal. ,vol. 394, pp. 575- 579 ,(2006) , 10.1042/BJ20051569
Maria J. Berry, Laila Banu, Yoyi Chen, Susan J. Mandel, J. David Kieffer, John W. Harney, P. Reed Larsen, Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3' untranslated region. Nature. ,vol. 353, pp. 273- 276 ,(1991) , 10.1038/353273A0