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Protocols

RibEx specifications

Information


Unique identifier OMICS_05299
Name RibEx
Alternative name Riboswitch Explorer
Interface Web user interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Enrique Merino

Publication for Riboswitch Explorer

RibEx citations

 (19)
call_split

Repression of branched chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine rich attenuator peptide

2018
PLoS Genet
PMCID: 5794164
PMID: 29357354
DOI: 10.1371/journal.pgen.1007159
call_split See protocol

[…] Putative terminator structures in the ilvD 5’UTR were identified using the predictive software RibEx [] and RNAfold []. Mfold [] was used to identify putative antiterminator sequences. RNAfold and Mfold were used to search for conserved T-box riboswitch features. T-box riboswitch multiple seque […]

library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] at RiboSW was not identified, and 12 instances in which the opposite was true.In 2009, Singh and collaborators compared the performance of HMM with other two CM web-based tools (Riboswitch finder and RibEx) in the search for ten riboswitches families on Rfam or RefSeq databases (Singh et al., ). Their results showed that HMM models run faster than CM and were more accurate than Riboswitch Finder a […]

library_books

The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA system

2017
PLoS Genet
PMCID: 5338858
PMID: 28212376
DOI: 10.1371/journal.pgen.1006629

[…] -binding region upstream the thi-operon of L. pneumophila (lpp1522-1527) and a structure with similarity to a THI-box sequence of the TPP riboswitch in the 5'UTR region () that was also identified by RibEx analysis []. Additionally, a putative Rho-independent terminator is located directly downstream of the TPP riboswitch (). EMSA assays with the in vitro transcribed 5'UTR RNA region and purified […]

library_books

Differential regulation of riboflavin supply genes in Vibrio cholerae

2017
PMCID: 5312566
PMID: 28239422
DOI: 10.1186/s13099-017-0159-z

[…] ortholog in Vibrio vulnificus. Importantly, the intergenic region between ribA-COG3236 and ribH is relatively large (264 bp) and conserves an apparently incomplete FMN riboswitch, as detected by the RIBEX software []. Thus, it is not possible to predict hiterto if these genes form an operon. Genes ribB and a second ortholog of ribA, hereafter referred to as ribA2, were identified in different reg […]

library_books

Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum

2016
Microb Genom
PMCID: 5320689
PMID: 28348850
DOI: 10.1099/mgen.0.000055

[…] fact that the traA.2 gene neighbouring msa2 was not duplicated in any isolates.It remains unknown whether msa loci are differentially regulated. Using the terminator prediction tool ARNold () and the RibEx riboswitch explorer (), we discovered that the palindrome at the 3' of the msa ORF contained a predicted rho-independent terminator/riboswitch-like element at both the msa loci, although with ‘G […]

library_books

Yersinia pestis and Yersinia pseudotuberculosis infection: a regulatory RNA perspective

2015
Front Microbiol
PMCID: 4585118
PMID: 26441890
DOI: 10.3389/fmicb.2015.00956

[…] TR regions >200 nucleotides in length which make them prime candidates to encode cis-acting regulatory elements like riboswitches. A bioinformatic search for riboswitch-like elements (RLEs) using the RibEx riboswitch explorer () predicted four known and an additional 17 RLEs involved in metabolic and gene expression functions, within these long 5′-UTRs. An example of this is that the mRNA of the b […]

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RibEx institution(s)
Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Morelos, México

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