Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

Journal of Molecular Biology
David H Mathews, Douglas H Turner

Abstract

With the rapid increase in the size of the genome sequence database, computational analysis of RNA will become increasingly important in revealing structure-function relationships and potential drug targets. RNA secondary structure prediction for a single sequence is 73 % accurate on average for a large database of known secondary structures. This level of accuracy provides a good starting point for determining a secondary structure either by comparative sequence analysis or by the interpretation of experimental studies. Dynalign is a new computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. It uses a dynamic programming construct suggested by Sankoff. Dynalign, however, restricts the maximum distance, M, allowed between aligned nucleotides in the two sequences. This makes the calculation tractable because the complexity is simplified to O(M(3)N(3)), where N is the length of the shorter sequence. The accuracy of Dynalign was tested with sets of 13 tRNAs, seven 5 S rRNAs, and two R2 3' UTR sequences. On average, Dynalign predicted 86.1 % of kn...Continue Reading

Citations

Oct 6, 2005·Biochemistry·Ilyas Yildirim, Douglas H Turner
Mar 18, 2006·Nucleosides, Nucleotides & Nucleic Acids·Wayne DawsonKenji Yamamoto
Apr 26, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·J Waldispühl, P Clote
Mar 27, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Morgan BishopThomas E Renz
Dec 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·P Clote
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Vineet BafnaShaojie Zhang
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mathias MöhlRolf Backofen
Jul 24, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Michal Ziv-UkelsonRon Shamir
Oct 17, 2009·Briefings in Functional Genomics & Proteomics·Stephan H Bernhart, Ivo L Hofacker
Sep 21, 2004·Bioinformatics·Sam Griffiths-Jones
Jan 20, 2005·Bioinformatics·Jakob Hull HavgaardJan Gorodkin
Dec 17, 2005·Bioinformatics·Zizhen YaoWalter L Ruzzo
Dec 17, 2005·Bioinformatics·Peter SteffenRobert Giegerich
Apr 27, 2007·Bioinformatics·Hisanori KiryuKiyoshi Asai
Jul 1, 2008·Bioinformatics·Chuong B DoSerafim Batzoglou
Sep 18, 2008·Bioinformatics·Robert K BradleyIan Holmes
Feb 5, 2009·Bioinformatics·Steffen HeyneRolf Backofen
Oct 4, 2011·Bioinformatics·Diana L Kolbe, Sean R Eddy
Jan 31, 2012·Bioinformatics·Matthew G Seetin, David H Mathews
Oct 13, 2012·Bioinformatics·Kengo SatoYasubumi Sakakibara
Apr 27, 2013·Bioinformatics·Thomas SchnattingerHans A Kestler
Nov 25, 2003·Nucleic Acids Research·Marcel FreundHeiner Schaal
Jun 25, 2004·Nucleic Acids Research·Jianhua RuanWeixiong Zhang
Jun 28, 2005·Nucleic Acids Research·P Clote
Jun 28, 2005·Nucleic Acids Research·Jakob H HavgaardJan Gorodkin
Apr 30, 2005·Nucleic Acids Research·Paul P GardnerStefan Washietl
Oct 6, 2006·Nucleic Acids Research·Björn Voss
Oct 7, 2008·Nucleic Acids Research·Stefan E SeemannRolf Backofen
Jan 6, 2010·Nucleic Acids Research·Stéfan Engelen, Fariza Tahi
Jun 18, 2009·Nucleic Acids Research·Jerome WaldispühlPeter Clote
Dec 6, 2011·Nucleic Acids Research·Zhenjiang XuDavid H Mathews
Apr 27, 2013·Nucleic Acids Research·Stanislav BellaousovDavid H Mathews
Aug 6, 2010·Cold Spring Harbor Perspectives in Biology·David H MathewsDouglas H Turner

❮ Previous
Next ❯

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.