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ERPIN specifications

Information


Unique identifier OMICS_07084
Name ERPIN
Alternative name Easy RNA Profile IdentificatioN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 5.4
Stability Stable
Maintained No

Versioning


No version available

Publication for Easy RNA Profile IdentificatioN

ERPIN citations

 (28)
library_books

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

2017
BMC Genomics
PMCID: 5746004
PMID: 29281966
DOI: 10.1186/s12864-017-4387-x

[…] s a stem-loop structure followed by a poly-T sequence [, ]. Rho-independent transcriptional termination signals can be predicted by particular on-line tools such as ARNold, which employs RNAMotif and Erpin tools (http://rna.igmors.u-psud.fr/toolbox/arnold/) [].Bifidobacteria enjoy an ever increasing scientific interest due to the purported beneficial effects they elicit on their (human) host []. H […]

library_books

A Genome Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R

2017
Front Microbiol
PMCID: 5596092
PMID: 28943874
DOI: 10.3389/fmicb.2017.01730

[…] dent terminators were implemented with RNAMotif 3.0.7 (http://casegroup.rutgers.edu/casegr-sh-2.5.html), TransTermHP 2.09 (transterm.cbcb.umd.edu/), FindTerm 2.4.3.1111 (http://www.molquest.com/) and Erpin 5.4 (http://tagc.univ-mrs.fr/erpin/). Searches for known functional RNA sequences among the predicted sRNAs were conducted within the Rfam database using Rfam, version 12.0 (http://rfam.xfam.org […]

library_books

Iron regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth

2017
BMC Genomics
PMCID: 5399841
PMID: 28431495
DOI: 10.1186/s12864-017-3684-8

[…] ′ and 3′ to each putative sRNA. These regions were screened for the presence of putative promoter motif using Promoter Prediction by PBROM (Softberry) [] and a rho independent terminator with ARNold (Erpin and RNAmotif programs). For prediction of FB motifs in FA 1090, we used a training set of 23 sequences previously shown to bind Fur in vitro by EMSA and/or in vivo in a FurTA assay to generate a […]

library_books

The isolation and characterization of Stenotrophomonas maltophilia T4 like bacteriophage DLP6

2017
PLoS One
PMCID: 5349666
PMID: 28291834
DOI: 10.1371/journal.pone.0173341

[…] ontains many proteins involved in DNA replication and homologous recombination.Rho-independent transcription termination sites were discovered using ARNold, which utilizes two complementary programs, Erpin [] and RNAmotif []. Of the 54 potential termination sites identified, only 19 were retained as authentic because they had a ΔG of -10 kcal/mol or less (). The 19 terminators were found downstrea […]

library_books

Characterization of Novel Bacteriophages for Biocontrol of Bacterial Blight in Leek Caused by Pseudomonas syringae pv. porri

2016
Front Microbiol
PMCID: 4791379
PMID: 27014204
DOI: 10.3389/fmicb.2016.00279

[…] ograms ARAGORN and tRNAscanSE (Lowe and Eddy, ; Laslett and Canback, ). Rho-independent terminators were predicted with ARNold, a search program that combines two complementary programs: RNAMotif and Erpin (Gautheret and Lambert, ; Macke et al., ). Probable promoter sequences were identified by looking for conserved intergenic motifs in the 100 bp upstream of every ORF with MEME and PHIRE (Lavigne […]

library_books

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

2016
BMC Genomics
PMCID: 4710047
PMID: 26753530
DOI: 10.1186/s12864-016-2376-0

[…] RNAspace platform were restricted to comparative analysis and homology searches using BLAST/ YASS (sequence homology tools) against the Rfam 10.0 seed database and three RNA motif search tools, DARN, ERPIN and INFERNAL. In total, 68 sRNAs representing true (and/or known), previously described sRNA sequences were assigned into 6 functional classes (E-value < 0.001), and these included: 1 ribozyme, […]

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ERPIN institution(s)
CNRS UMR 6207, Université de la Méditerranée, Marseille, France

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