Rose: generating sequence families

Bioinformatics
J StoyeF Meyer

Abstract

We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs. The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes. Rose is available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available upon request. folker@TechFak.Uni-Bielefeld.DE

Citations

Jun 6, 2006·Journal of Molecular Evolution·Jason EvansJames Foster
Oct 5, 2007·Journal of Biosciences·Abha S BaisMartin Vingron
Jul 2, 2005·Biochimica Et Biophysica Acta·Tobias HillHelgi B Schiöth
Feb 19, 2013·Computers in Biology and Medicine·Xiangyuan ZhuAhmad Salah
Jun 21, 2005·Current Opinion in Structural Biology·Iain M WallaceDesmond G Higgins
May 23, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mathieu BlanchetteMartin Tompa
Apr 26, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Valery PolyanovskyVladimir G Tumanyan
Dec 8, 2005·Bioinformatics·Tanja Gesell, Arndt von Haeseler
Mar 3, 2006·Bioinformatics·Hannes Luz, Martin Vingron
Jan 24, 2007·Bioinformatics·Abha Singh BaisMartin Vingron
Sep 7, 2006·Bioinformatics·Usman Roshan, Dennis R Livesay
Feb 3, 2007·Bioinformatics·Robert G Beiko, Robert L Charlebois
Mar 3, 2007·Bioinformatics·Jason S Papadopoulos, Richa Agarwala
Jan 17, 2009·Bioinformatics·Fuxia ChengTodd J Vision
Jun 10, 2009·Bioinformatics·Salvador Capella-GutiérrezToni Gabaldón
Mar 2, 2010·Bioinformatics·Eduardo CorelBurkhard Morgenstern
Aug 15, 2008·Molecular Biology and Evolution·Victor Soria-Carrasco, Jose Castresana
Apr 21, 2009·Molecular Biology and Evolution·Morgan N PriceAdam P Arkin
May 9, 2009·Molecular Biology and Evolution·William Fletcher, Ziheng Yang
Aug 5, 2009·Molecular Biology and Evolution·Cory L StropeEtsuko N Moriyama
Mar 9, 2010·Molecular Biology and Evolution·Osnat PennTal Pupko
Dec 14, 2011·Molecular Biology and Evolution·Daniel A DalquenChristophe Dessimoz
Mar 3, 2012·Molecular Biology and Evolution·Tina KoestlerIngo Ebersberger
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 24, 2010·Nucleic Acids Research·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
May 26, 2010·Nucleic Acids Research·Osnat PennTal Pupko
Jul 20, 2010·Nucleic Acids Research·Mohamed Radhouene AnibaJulie D Thompson
Mar 26, 2003·Genome Research·Michael BrudnoSerafim Batzoglou
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Tero AittokallioRiitta Lahesmaa
Feb 28, 2009·BMC Bioinformatics·Feng YueJijun Tang
Jan 28, 2010·BMC Bioinformatics·Jaebum Kim, Saurabh Sinha
May 24, 2011·BMC Bioinformatics·Catherine L AndersonEtsuko N Moriyama
Mar 5, 2011·BMC Bioinformatics·Giltae SongWebb Miller
Dec 22, 2011·BMC Bioinformatics·Jimmy Yang, Tandy Warnow
Aug 30, 2012·BMC Bioinformatics·Anna M Kedzierska, Marta Casanellas
Jun 28, 2013·BMC Bioinformatics·Joel SjöstrandBengt Sennblad
Dec 25, 2003·BMC Bioinformatics·Michael BrudnoBurkhard Morgenstern
Jan 23, 2004·BMC Bioinformatics·Daniel A PollardMichael B Eisen
Apr 29, 2005·BMC Bioinformatics·Erik L L Sonnhammer, Volker Hollich
Aug 10, 2005·BMC Bioinformatics·Chunlin Wang, Elliot J Lefkowitz
Sep 29, 2005·BMC Bioinformatics·Andy PangElisabeth R M Tillier

❮ 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.