PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures

Genome Biology
Mirko Ledda, Sharon Aviran

Abstract

Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions.

References

Nov 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·R Nussinov, A B Jacobson
Jan 1, 1997·Biopolymers·S R Holbrook, S H Kim
Apr 1, 2000·RNA·C FlammP Schuster
May 23, 2001·Nucleic Acids Research·J GorodkinG D Stormo
May 7, 2002·RNA·Magnus LindellE Gerhart H Wagner
Jul 20, 2002·Current Opinion in Structural Biology·Robin R GutellJamie J Cannone
Nov 5, 2002·Methods : a Companion to Methods in Enzymology·Jason Jon FritzLynn Shaw
Oct 3, 2003·Chembiochem : a European Journal of Chemical Biology·Boris FürtigHarald Schwalbe
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·David H MathewsDouglas H Turner
Oct 2, 2004·BMC Bioinformatics·Paul P Gardner, Robert Giegerich
Apr 7, 2005·Current Opinion in Chemical Biology·Thomas D Tullius, Jason A Greenbaum
Jul 27, 2005·RNA·Magnus LindellLeif A Kirsebom
Dec 17, 2005·Bioinformatics·Zizhen YaoWalter L Ruzzo
Jan 28, 2006·FEMS Microbiology Reviews·Franz NarberhausSaheli Chowdhury
May 19, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jesper JanssonWing-Kin Sung
Aug 19, 2007·Journal of Mathematical Biology·Michael SarverNeocles B Leontis
Sep 7, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Isana Veksler-LublinskyKlara Kedem
Sep 26, 2007·Nature Genetics·Michael KerteszEran Segal
Oct 20, 2007·Nature Protocols·Pilar TijerinaRick Russell
Dec 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Katherine E DeiganKevin M Weeks
Feb 26, 2009·Cell·Phillip A Sharp
Mar 25, 2009·Bioinformatics·Eric P NawrockiSean R Eddy
Mar 17, 2010·BMC Bioinformatics·Jessica S Reuter, David H Mathews
May 28, 2010·RNA·Ivo L HofackerPeter F Stadler
Jun 18, 2010·Methods : a Companion to Methods in Enzymology·Justin T Low, Kevin M Weeks
Sep 3, 2010·PLoS Genetics·Matthew HalvorsenAlain Laederach
Nov 26, 2010·Cold Spring Harbor Perspectives in Biology·Ronald R Breaker
May 10, 2011·Nature Methods·José Almeida Cruz, Eric Westhof
Jun 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sharon AviranLior Pachter
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Dec 24, 2011·Science·Jenny L BakerRonald R Breaker
Jun 13, 2012·Bioinformatics·Steffen HeyneRolf Backofen
Jul 4, 2012·BMC Research Notes·M Shel SwensonChristine E Heitsch
Jan 18, 2013·Nucleic Acids Research·Zsuzsanna SükösdChristine E Heitsch
Mar 19, 2013·Proceedings of the National Academy of Sciences of the United States of America·Christine E HajdinKevin M Weeks
Apr 23, 2013·Algorithms for Molecular Biology : AMB·Sebastian WillRolf Backofen
Jun 22, 2013·Current Protocols in Chemical Biology·Stefanie A MortimerJulius B Lucks
Aug 10, 2013·Methods : a Companion to Methods in Enzymology·Irina V NovikovaKarissa Y Sanbonmatsu
Sep 7, 2013·Bioinformatics·Eric P Nawrocki, Sean R Eddy
May 14, 2014·Nature Reviews. Genetics·Stefanie A MortimerJennifer A Doudna

❮ Previous
Next ❯

Citations

Nov 22, 2018·PloS One·Sana VaziriSharon Aviran
Nov 30, 2018·Wiley Interdisciplinary Reviews. RNA·Elodie MaillerValerie Vivet-Boudou
Feb 23, 2019·Genome Biology·Krishna ChoudharySharon Aviran
Aug 28, 2021·NAR Genomics and Bioinformatics·Pierce RadeckiSharon Aviran

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
SHAPE-seq

Software Mentioned

RNAprob
- LEARN
Ensemble
RNAstructure
GTfold
patteRNA
ViennaRNA
SCIKIT

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Methods in Molecular Biology
Oliviero Carugo
Molecular Diagnosis : a Journal Devoted to the Understanding of Human Disease Through the Clinical Application of Molecular Biology
M P DiGiovanna
Proceedings of the National Academy of Sciences of the United States of America
Michael Q Zhang
Health Data Management
Elizabeth Gardner
© 2022 Meta ULC. All rights reserved