Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

Mohammad Reza Naghdi 1 Katia Smail 1 Joy X Wang 2 Fallou Wade 1 Ronald R Breaker 2 Jonathan Perreault 1, *
* Corresponding author
1 INRS-IAF - Institut Armand Frappier
2 Department of Molecular, Cellular, and Developmental Biology
Abstract : The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale. Here we present various approaches using the database RiboGap as a primary tool for finding known ncRNAs and for uncovering simple sequence motifs with regulatory roles. This database also can be used to easily extract intergenic sequences of eubacteria and archaea to find conserved RNA structures upstream of given genes. We also show how to extend analysis further to choose the best candidate ncRNAs for experimental validation.
Keywords : Rfam Methyltransferase RNA secondary structure Bioinformatics CsrA GraphClust Infernal Riboswitch RsmA TRAP ncRNA
Document type :
Journal articles
Complete list of metadatas
https://hal-pasteur.archives-ouvertes.fr/pasteur-01533970
Contributor : Michel Courcelles <>
Submitted on : Tuesday, June 6, 2017 - 10:13:25 PM
Last modification on : Monday, October 8, 2018 - 5:44:05 PM

Links full text

openaccess

Identifiers

Collections

PASTEUR | RIIP | INRS-IAF

Citation

Mohammad Reza Naghdi, Katia Smail, Joy X Wang, Fallou Wade, Ronald R Breaker, et al.. Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.. Methods, Elsevier, 2017, 117, pp.3-13. ⟨10.1016/j.ymeth.2017.02.009⟩. ⟨pasteur-01533970⟩

Export

BibTeX TEI DC DCterms EndNote

Share

Metrics

Record views

76

Contact

support.ccsd.cnrs.fr
hal.support@ccsd.cnrs.fr
Logo CCSD