ArticleNucleic acids research2013
SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 119 citations in OpenAlex.
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- Recent advances in exploring the composition and evolution of the prokaryotic selenoproteome.Applied and environmental microbiology · 2026Review
- BSepDB: a database of bacterial selenoprotein genes and proteins.BMC genomics · 2026Article
- Expanding the genetic code: phage-driven evolution of pyrrolysyl-synthetase for site-specific incorporation of synthetic phenylalanine and tyrosine derivatives.Frontiers in molecular biosciences · 2026Article
- Running a genetic stop sign accelerates oxygen metabolism and energy production in horses.Science (New York, N.Y.) · 2025Article
- Pyrrolysine Aminoacyl-tRNA Synthetase as a Tool for Expanding the Genetic Code.International journal of molecular sciences · 2025Review
- Water-Soluble Se-Containing Proteins from Chicken Alleviate DSS-Induced Ulcerative Colitis in Mice via Inhibiting TLR4/MyD88 Pathway and Protecting the Goblet Cell Pathway.Biological trace element research · 2024Article
- Asgard archaea modulate potential methanogenesis substrates in wetland soil.Nature communications · 2024Article
- A DIO2 missense mutation and its impact on fetal response to PRRSV infection.BMC veterinary research · 2024Article
- GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins.Genome biology · 2023Article
- Eight Unexpected Selenoprotein Families in Organometallic Biochemistry in Clostridium difficile, in ABC Transport, and in Methylmercury Biosynthesis.Journal of bacteriology · 2023Article
- Design of typical genes for heterologous gene expression.Scientific reports · 2022Article
- Chemoproteomic interrogation of selenocysteine by low-pH isoTOP-ABPP.Methods in enzymology · 2022Article
- An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes.Molecular biology and evolution · 2021Article
- Larval metamorphosis is inhibited by methimazole and propylthiouracil that reveals possible hormonal action in the mussel Mytilus coruscus.Scientific reports · 2021Article
- Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages.ISME communications · 2021Article
- Xenopus laevis and human type 3 iodothyronine deiodinase enzyme cross-species sensitivity to inhibition by ToxCast chemicals.Toxicology in vitro : an international journal published in association with BIBRA · 2021Article
- An unusual thioredoxin system in the facultative parasite Acanthamoeba castellanii.Cellular and molecular life sciences : CMLS · 2021Article
- Programmed Deviations of Ribosomes From Standard Decoding in Archaea.Frontiers in microbiology · 2021Review
- The algal selenoproteomes.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3' UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.