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RRE specifications

Information


Unique identifier OMICS_26391
Name RRE
Alternative name Retrieval Regulative Elements
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Raffaele A. Calogero

Additional information


To run RRE, it is necessary to download from NCBI .gbs and .fa or .gbk files related to the organism of interest. Web application: https://www6.unito.it/RRE/EN/

Information


Unique identifier OMICS_26391
Name RRE
Alternative name Retrieval Regulative Elements
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output format FASTA,HTML,XML
Operating system Unix/Linux, Windows
Programming languages Java
Database management system MySQL
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Raffaele A. Calogero

Additional information


To run RRE, it is necessary to download from NCBI .gbs and .fa or .gbk files related to the organism of interest. Web application: https://www6.unito.it/RRE/EN/

Publication for Retrieval Regulative Elements

RRE citations

 (3)
library_books

AP 2α regulates migration of GN 11 neurons via a specific genetic programme involving the Axl receptor tyrosine kinase

2009
BMC Biol
PMCID: 2700071
PMID: 19463168
DOI: 10.1186/1741-7007-7-25

[…] nd the putative AP-2 binding sites were analysed by using the ENSEMBL bank database [] and the canonical AP-2α PWM []. The Retrieval of non-coding Regulative Elements from annotated genome databases (RRE) software was used to design primer pairs to perform chromatin immunoprecipitation analysis for the Axl gene. RRE is available at [] (see also []). […]

library_books

WebScipio: An online tool for the determination of gene structures using protein sequences

2008
BMC Genomics
PMCID: 2644328
PMID: 18801164
DOI: 10.1186/1471-2164-9-422

[…] , identifying all homologous genes, and predicting their gene structures.To retrieve gene data and non-coding sequence, some programs and web-tools are available. The Retrieval of Regulative Regions (RRE) tool is a Java application which parses annotation and homology data from NCBI []. RRE is available as a web application, which however only hosts a small number of eukaryotic genomes and annotat […]

library_books

Non coding sequence retrieval system for comparative genomic analysis of gene regulatory elements

2007
BMC Bioinformatics
PMCID: 1838437
PMID: 17362514
DOI: 10.1186/1471-2105-8-94

[…] NCSRS) that performs the automated retrieval of non-coding sequences among genomes of different species. A previously developed application for retrieving NCS, called Retrieval of Regulative Regions (RRE) [] parses annotation and homology data from NCBI to identify NCS. This parser requires local installation but also requires a local copy of desired genomes and annotation files. A web based appli […]

Citations

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RRE institution(s)
Department of Informatics, University of Piemonte Orientale ‘Amedeo Avogadro’, Alessandria, Italy; Department of Informatics University of Torino, Torino, Italy; Department of Clinical and Biological Sciences University of Torino, Orbassano, Italy
RRE funding source(s)
Supported by a PRIN 2002053274 grant, and partially by PRIN 2001057147, FIRB RBAU01JTHS and RBNE0157EH grants from the Italian Ministry for the Universities and Scientific and Technical Research (MIUR).

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