STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time

Bioinformatics
Deniz DalliGerhard Steger

Abstract

Alignment of RNA has a wide range of applications, for example in phylogeny inference, consensus structure prediction and homology searches. Yet aligning structural or non-coding RNAs (ncRNAs) correctly is notoriously difficult as these RNA sequences may evolve by compensatory mutations, which maintain base pairing but destroy sequence homology. Ideally, alignment programs would take RNA structure into account. The Sankoff algorithm for the simultaneous solution of RNA structure prediction and RNA sequence alignment was proposed 20 years ago but suffers from its exponential complexity. A number of programs implement lightweight versions of the Sankoff algorithm by restricting its application to a limited type of structure and/or only pairwise alignment. Thus, despite recent advances, the proper alignment of multiple structural RNA sequences remains a problem. Here we present StrAl, a heuristic method for alignment of ncRNA that reduces sequence-structure alignment to a two-dimensional problem similar to standard multiple sequence alignment. The scoring function takes into account sequence similarity as well as up- and downstream pairing probability. To test the robustness of the algorithm and the performance of the program, we ...Continue Reading

References

Jul 1, 1991·Computer Applications in the Biosciences : CABIOS·D K Chiu, T Kolodziejczak
Jan 1, 1990·Methods in Enzymology·M GribskovD Eisenberg
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Apr 21, 1995·Journal of Molecular Biology·D GautheretR R Gutell
Jan 1, 1993·European Biophysics Journal : EBJ·S BonhoefferP Schuster
Feb 1, 1994·Computer Applications in the Biosciences : CABIOS·J D ThompsonT J Gibson
Jun 1, 1993·Computer Applications in the Biosciences : CABIOS·O Gotoh
Feb 2, 1999·Journal of Molecular Biology·E Rivas, S R Eddy
Jun 22, 1999·Nucleic Acids Research·J D ThompsonO Poch
Aug 27, 1999·Advances in Biophysics·O Gotoh
Feb 10, 2000·Molecular Biology and Evolution·W J BrunoA L Halpern
Jun 14, 2000·Current Opinion in Structural Biology·M Zuker
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Dec 6, 2001·Nature Reviews. Genetics·S R Eddy
Mar 21, 2002·Journal of Molecular Biology·David H Mathews, Douglas H Turner
May 23, 2002·Science·Gisela Storz
Jun 25, 2002·Journal of Molecular Biology·Ivo L HofackerPeter F Stadler
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Jun 26, 2003·Nucleic Acids Research·Bjarne Knudsen, Jotun Hein
Jun 26, 2003·Nucleic Acids Research·Ivo L Hofacker
Jul 25, 2003·Molecular Phylogenetics and Evolution·Cendrine HudelotPaul G Higgs
Aug 13, 2003·Bioinformatics·Ari Löytynoja, Michel C Milinkovitch
Sep 23, 2003·BMC Bioinformatics·Robert J Klein, Sean R Eddy
Apr 10, 2004·Bioinformatics·Ivo L HofackerPeter F Stadler
Apr 24, 2004·EMBO Reports·Gregory V Kryukov, Vadim N Gladyshev
Jan 20, 2005·Bioinformatics·Jakob Hull HavgaardJan Gorodkin
Jan 22, 2005·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jan 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Stefan WashietlPeter F Stadler
Mar 26, 2005·BMC Bioinformatics·Ian Holmes
Apr 30, 2005·Nucleic Acids Research·Aurélie LescouteEric Westhof
Apr 30, 2005·Nucleic Acids Research·Paul P GardnerStefan Washietl
May 26, 2005·Trends in Genetics : TIG·Susan Gottesman
Jun 16, 2005·Nature Reviews. Molecular Cell Biology·Martha J Fedor, James R Williamson
Jun 28, 2005·Nucleic Acids Research·Jakob H HavgaardJan Gorodkin
Sep 13, 2005·Annual Review of Microbiology·Wade C Winkler, Ronald R Breaker
Sep 15, 2005·Bioinformatics·L C MartinL M Wahl

❮ Previous
Next ❯

Citations

Jul 10, 2007·Journal of Mathematical Biology·Kengo SatoYasubumi Sakakibara
Nov 4, 2008·Molecular Biotechnology·Ajish D George, Scott A Tenenbaum
Feb 28, 2007·Bioinformatics·Elfar TorarinssonJan Gorodkin
Jul 1, 2008·Bioinformatics·Chuong B DoSerafim Batzoglou
Aug 4, 2010·Bioinformatics·Akito Taneda
Oct 13, 2012·Bioinformatics·Kengo SatoYasubumi Sakakibara
Apr 19, 2008·Nucleic Acids Research·Andreas WilmCédric Notredame
May 17, 2008·Nucleic Acids Research·Sébastien MorettiCédric Notredame
Sep 3, 2009·Nucleic Acids Research·Roman R StocsitsPeter F Stadler
Apr 26, 2011·Nucleic Acids Research·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Aug 24, 2007·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Oya Yazgan, Jocelyn E Krebs
Mar 5, 2011·BMC Bioinformatics·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Jul 20, 2013·BMC Bioinformatics·Fernando MeyerMichael Beckstette
Jul 17, 2007·BMC Bioinformatics·Matthias Kruspe, Peter F Stadler
Apr 30, 2008·BMC Bioinformatics·Andreas WilmGerhard Steger
Jan 25, 2008·BMC Bioinformatics·Yasuo TabeiKiyoshi Asai
Nov 19, 2008·BMC Bioinformatics·Stephan H BernhartPeter F Stadler
Oct 26, 2006·Algorithms for Molecular Biology : AMB·Andreas WilmGerhard Steger
Apr 21, 2009·Bioinformatics·Yasuo Tabei, Kiyoshi Asai
Mar 9, 2010·New Biotechnology·Benoît MasquidaFabrice Jossinet
Dec 9, 2014·Journal of Molecular and Cellular Cardiology·Meik KunzThomas Dandekar
Jun 6, 2007·Current Opinion in Microbiology·Fabrice JossinetEric Westhof
May 18, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Daniel DeBlasioShaojie Zhang
Mar 20, 2013·International Journal of Molecular Sciences·Haruka YonemotoMichiaki Hamada
Dec 30, 2017·Genome Biology·Martin A SmithJohn S Mattick
Dec 9, 2010·BMC Bioinformatics·Yutaka SaitoYasubumi Sakakibara
Jun 21, 2016·Current Protocols in Bioinformatics·Lars BarquistPaul P Gardner
Nov 29, 2015·Briefings in Bioinformatics·Maria ChatzouCedric Notredame
Jan 15, 2013·Human Mutation·Radhakrishnan SabarinathanJan Gorodkin

❮ 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.