A fast structural multiple alignment method for long RNA sequences

BMC Bioinformatics
Yasuo TabeiKiyoshi Asai


Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been proposed, they are either inaccurate or computationally too expensive. Faster methods with reasonable accuracies are required for genome-scale analyses. We propose a fast algorithm for multiple structural alignments of RNA sequences that is an extension of our pairwise structural alignment method (implemented in SCARNA). The accuracies of the implemented software, MXSCARNA, are at least as favorable as those of state-of-art algorithms that are computationally much more expensive in time and memory. The proposed method for structural alignment of multiple RNA sequences is fast enough for large-scale analyses with accuracies at least comparable to those of existing algorithms. The source code of MXSCARNA and its web server are available at http://mxscarna.ncrna.org.


Oct 20, 1975·Biochimica Et Biophysica Acta·B W Matthews
Jun 6, 1998·Bioinformatics·B MorgensternT Werner
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ian Holmes, R Durbin
May 18, 1999·Journal of Molecular Biology·David H MathewsD H Turner
Jun 22, 1999·Nucleic Acids Research·J D ThompsonO Poch
Aug 31, 2000·Journal of Molecular Biology·Cedric NotredameJ Heringa
Jun 25, 2002·Journal of Molecular Biology·Ivo L HofackerPeter F Stadler
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jan 10, 2003·Nucleic Acids Research·Magnus Alm RosenbladTore Samuelsson
Jan 10, 2003·Nucleic Acids Research·Sam Griffiths-JonesS R Eddy
Jun 26, 2003·Nucleic Acids Research·Bjarne Knudsen, Jotun Hein
Sep 23, 2003·BMC Bioinformatics·Robert J Klein, S R Eddy
Apr 10, 2004·Bioinformatics·Ivo L HofackerPeter F Stadler
Oct 2, 2004·BMC Bioinformatics·Paul P Gardner, Robert Giegerich
Oct 28, 2004·BMC Bioinformatics·Ian Holmes
Feb 3, 2005·Genome Research·Chuong B DoSerafim Batzoglou
Apr 30, 2005·Nucleic Acids Research·Paul P GardnerStefan Washietl
Dec 17, 2005·Bioinformatics·Zizhen YaoWalter L Ruzzo
Aug 16, 2006·Bioinformatics·Michiaki HamadaKiyoshi Asai
Nov 15, 2006·BMC Bioinformatics·Philipp N SeibelMatthias Wolf
Feb 28, 2007·Bioinformatics·Elfar TorarinssonJ Gorodkin
Apr 17, 2007·PLoS Computational Biology·Sebastian WillRolf Backofen
Apr 27, 2007·Bioinformatics·Hisanori KiryuKiyoshi Asai
Dec 7, 2007·Bioinformatics·Hisanori KiryuKiyoshi Asai


Nov 4, 2008·Molecular Biotechnology·Ajish D George, Scott A Tenenbaum
Sep 18, 2008·Bioinformatics·Robert K BradleyIan Holmes
Dec 20, 2008·Bioinformatics·Michiaki HamadaKiyoshi Asai
May 30, 2009·Bioinformatics·Michiaki HamadaKiyoshi Asai
Oct 10, 2012·Bioinformatics·Jana SperschneiderMichael J Wise
Oct 13, 2012·Bioinformatics·Kengo SatoYasubumi Sakakibara
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Apr 29, 2008·Nucleic Acids Research·Kiyoshi AsaiToutai Mituyama
Sep 3, 2009·Nucleic Acids Research·Roman R StocsitsPeter F Stadler
Sep 17, 2010·Nucleic Acids Research·Michiaki HamadaKiyoshi Asai
Apr 26, 2011·Nucleic Acids Research·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Dec 2, 2010·Journal of Bioinformatics and Computational Biology·Vandanaben PatelKaizhong Zhang
May 4, 2010·BMC Bioinformatics·Andreas BremgesRobert Giegerich
Apr 22, 2011·BMC Bioinformatics·Arif O HarmanciDavid H Mathews
Mar 5, 2011·BMC Bioinformatics·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Apr 21, 2009·Bioinformatics·Yasuo Tabei, Kiyoshi Asai
Jan 1, 2012·FEBS Open Bio·Shoji OhuchiYoshikazu Nakamura
Aug 15, 2015·Biochimica Et Biophysica Acta·Junichi IwakiriKiyoshi Asai
Aug 6, 2009·Molecular Phylogenetics and Evolution·Harald O LetschBernhard Misof
Nov 22, 2015·Bioinformatics·Laura DiChiacchioDavid H Mathews
Dec 5, 2014·IEEE Transactions on Bio-medical Engineering·Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David Hoksza, Daniel Svozil
Aug 10, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jikai LeiYanni Sun
Oct 11, 2015·Biology Direct·Avinash Achar, Pål Sætrom
Apr 1, 2014·International Journal of Systematic and Evolutionary Microbiology·Juliana Velasco de Castro OliveiraDiego Mauricio Riaño-Pachón
Feb 5, 2015·BMC Genomics·Shermin PeiMichelle M Meyer
May 3, 2014·RNA Biology·Marcin MagnusJanusz M Bujnicki
Aug 1, 2015·PLoS Pathogens·Marçal MarinéGustavo Henrique Goldman
Jan 4, 2017·Journal of Chemical Theory and Computation·Asaminew H AytenfisuDavid H Mathews
Apr 20, 2017·International Journal of Molecular Sciences·Xuankun LiDing Yang
Jun 21, 2016·Current Protocols in Bioinformatics·Lars BarquistPaul P Gardner
Jun 29, 2018·Bioinformatics·Jean-Pierre Séhi Glouzon, Aïda Ouangraoua
Nov 29, 2015·Briefings in Bioinformatics·Maria ChatzouCedric Notredame

Methods Mentioned


Related Concepts

Trending Feeds


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.

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.

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.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Nodding Syndrome

Nodding Syndrome is a neurological and epileptiform disorder characterized by psychomotor, mental, and growth retardation. Discover the latest research on Nodding Syndrome here.

LRRK2 & Microtubules

Mutations in the LRRK2 gene are risk-factors for developing Parkinson’s disease (PD). LRRK2 mutations in PD have been shown to enhance its association with microtubules. Here is the latest research.