Selenoprotein prediction statistics

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Protocols

Selenoprotein prediction specifications

Information


Unique identifier OMICS_01566
Name Selenoprotein prediction
Interface Web user interface
Restrictions to use None
Input data Some nucleotide sequences.
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • Seblastian
  • SECISearch
  • SECISearch3

Publications for Selenoprotein prediction

Selenoprotein prediction citations

 (44)
library_books

The Anti Oxidant Defense System of the Marine Polar Ciliate Euplotes nobilii: Characterization of the MsrB Gene Family

2017
Biology
PMCID: 5371997
PMID: 28106766
DOI: 10.3390/biology6010004

[…] The nucleotide gene sequences and the functional domains of the deduced amino acid sequences were analyzed with the SECISearch tool (http://genome.unl.edu/SECISearch.html) and ScanProsite (http://prosite.expasy.org/), respectively. The amino acid sequences used to establish the En-MsrB phylogenetic relationships we […]

call_split

Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements

2016
Open Biol
PMCID: 5133445
PMID: 27881738
DOI: 10.1098/rsob.160241
call_split See protocol

[…] elenoprotein P genes were identified in vertebrate genomes using the program Selenoprofiles []. Their SECIS elements were identified by scanning the sequences downstream of the coding sequences using SECISearch3 []. The SECIS sequences were aligned with t-coffee [], and then visualized using Jalview []. The predicted phylogenetic tree of SECIS elements was computed based on sequence identity, usin […]

library_books

De novo assembly and analysis of changes in the protein coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water

2016
BMC Genomics
PMCID: 5100079
PMID: 27821072
DOI: 10.1186/s12864-016-3208-y

[…] full-length transcripts, it was evident that some of these sequences represented truncated forms due to the automated misinterpretation of putative Sec-encoding opal stop codons. With the aid of the Selenoprotein Prediction Server [], four putative full-length GPx candidates were identified. By comparison of the coding sequences it appears that two of these putative GPx sequences (TR41138|c2_g1_i […]

library_books

Evolutionary Dynamics of Abundant Stop Codon Readthrough

2016
Mol Biol Evol
PMCID: 5100048
PMID: 27604222
DOI: 10.1093/molbev/msw189

[…] the opposite strand, rather than by readthrough. We searched for SECIS elements in the 3′-UTRs of each of the remaining high-scoring second ORFs, extended to be at least 1,000 nucleotides long, using SECISearch3 () with the default parameters, and as a result excluded AGAP000358, an ortholog of the known Drosophila selenoprotein SelG, from our candidates list as a likely selenoprotein; SECISearch3 […]

library_books

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems

2016
Mol Biol Evol
PMCID: 4989117
PMID: 27413050
DOI: 10.1093/molbev/msw122

[…] nd, we ran blast searches () (tblastn program) using a comprehensive set of selenoproteins annotated in other species, and further manually inspected the results. Third, we used a modified version of Seblastian (). This program identifies potential SECIS elements as a first step, and then searches for known or novel selenoproteins in the sequence upstream of each SECIS, using blastx against a data […]

library_books

Overexpression of pig selenoprotein S blocks OTA induced promotion of PCV2 replication by inhibiting oxidative stress and p38 phosphorylation in PK15 cells

2016
Oncotarget
PMCID: 4991468
PMID: 26943035
DOI: 10.18632/oncotarget.7814

[…] As shown in Figure , the SECIS sequence in the pig SelS 3′-UTR was identified using SECISearch software (Figure ). Total RNA was extracted from pig kidney tissue and reversed transcribed into cDNA, which was then amplified with PCR using a SelS primer; electrophoresis showed that the […]

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