Comparing tandem repeats with duplications and excisions of variable degree
Sammeth M, Stoye J (2006)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(4): 395-407.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Sammeth, Michael;
Stoye, JensUniBi ![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
Einrichtung
Abstract / Bemerkung
Traditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysis knows a variety of more complex mutation events (e. g., duplications, excisions, and rearrangements), especially regarding DNA. With ever more DNA sequence data becoming available, the need to accurately compare sequences which have clearly undergone more complicated types of mutational processes is becoming critical. Herein we introduce a new method for pairwise alignment and comparison of sequences with respect to the special evolution of tandem repeats: substitutions and indels of single positions and, additionally, duplications and excisions of variable degree (i.e., of one or more repeat copies simultaneously) are taken into account. To evaluate our method, we apply it to the spa VNTR (variable number of tandem repeats) cluster of Staphylococcus aureus, a bacterium of high medical importance.
Stichworte
dynamic programming;
sequence comparison;
pairwise alignment;
tandem repeats;
repeat duplication history;
variable number of tandem repeats
Erscheinungsjahr
2006
Zeitschriftentitel
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Band
3
Ausgabe
4
Seite(n)
395-407
ISSN
1545-5963
Page URI
https://pub.uni-bielefeld.de/record/1597213
Zitieren
Sammeth M, Stoye J. Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2006;3(4):395-407.
Sammeth, M., & Stoye, J. (2006). Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(4), 395-407. https://doi.org/10.1109/TCBB.2006.46
Sammeth, Michael, and Stoye, Jens. 2006. “Comparing tandem repeats with duplications and excisions of variable degree”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3 (4): 395-407.
Sammeth, M., and Stoye, J. (2006). Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, 395-407.
Sammeth, M., & Stoye, J., 2006. Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(4), p 395-407.
M. Sammeth and J. Stoye, “Comparing tandem repeats with duplications and excisions of variable degree”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, 2006, pp. 395-407.
Sammeth, M., Stoye, J.: Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 3, 395-407 (2006).
Sammeth, Michael, and Stoye, Jens. “Comparing tandem repeats with duplications and excisions of variable degree”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3.4 (2006): 395-407.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
7 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Probabilistic approaches to alignment with tandem repeats.
Nánási M, Vinař T, Brejová B., Algorithms Mol Biol 9(1), 2014
PMID: 24580741
Nánási M, Vinař T, Brejová B., Algorithms Mol Biol 9(1), 2014
PMID: 24580741
A lossy compression technique enabling duplication-aware sequence alignment.
Freschi V, Bogliolo A., Evol Bioinform Online 8(), 2012
PMID: 22518086
Freschi V, Bogliolo A., Evol Bioinform Online 8(), 2012
PMID: 22518086
A probabilistic model for sequence alignment with context-sensitive indels.
Hickey G, Blanchette M., J Comput Biol 18(11), 2011
PMID: 21951055
Hickey G, Blanchette M., J Comput Biol 18(11), 2011
PMID: 21951055
WAMI: a web server for the analysis of minisatellite maps.
Abouelhoda M, El-Kalioby M, Giegerich R., BMC Evol Biol 10(), 2010
PMID: 20525398
Abouelhoda M, El-Kalioby M, Giegerich R., BMC Evol Biol 10(), 2010
PMID: 20525398
Why would phylogeneticists ignore computerized sequence alignment?
Morrison DA., Syst Biol 58(1), 2009
PMID: 20525575
Morrison DA., Syst Biol 58(1), 2009
PMID: 20525575
Alignment of minisatellite maps based on run-length encoding scheme.
Abouelhoda MI, Giegerich R, Behzadi B, Steyaert JM., J Bioinform Comput Biol 7(2), 2009
PMID: 19340916
Abouelhoda MI, Giegerich R, Behzadi B, Steyaert JM., J Bioinform Comput Biol 7(2), 2009
PMID: 19340916
Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms.
Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D., BMC Microbiol 7(), 2007
PMID: 17967176
Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D., BMC Microbiol 7(), 2007
PMID: 17967176
25 References
Daten bereitgestellt von Europe PubMed Central.
AUTHOR UNKNOWN, 0
Reconstructing the duplication history of tandemly repeated genes.
Elemento O, Gascuel O, Lefranc MP., Mol. Biol. Evol. 19(3), 2002
PMID: 11861887
Elemento O, Gascuel O, Lefranc MP., Mol. Biol. Evol. 19(3), 2002
PMID: 11861887
Topological rearrangements and local search method for tandem duplication trees.
Bertrand D, Gascuel O., IEEE/ACM Trans Comput Biol Bioinform 2(1), 2005
PMID: 17044161
Bertrand D, Gascuel O., IEEE/ACM Trans Comput Biol Bioinform 2(1), 2005
PMID: 17044161
Reconstructing the Duplication History of a Tandem Repeat
benson, Proc Int'l Conf Intelligent Systems for Microbiology (ISMB '99) (), 1999
benson, Proc Int'l Conf Intelligent Systems for Microbiology (ISMB '99) (), 1999
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
A Linear Algorithm for the Detection of Evolutive Tandem Repeats
groult, Proc Prague Stringology Conf (), 2003
groult, Proc Prague Stringology Conf (), 2003
A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis.
Le Fleche P, Hauck Y, Onteniente L, Prieur A, Denoeud F, Ramisse V, Sylvestre P, Benson G, Ramisse F, Vergnaud G., BMC Microbiol. 1(), 2001
PMID: 11299044
Le Fleche P, Hauck Y, Onteniente L, Prieur A, Denoeud F, Ramisse V, Sylvestre P, Benson G, Ramisse F, Vergnaud G., BMC Microbiol. 1(), 2001
PMID: 11299044
Evolutionary models of the emergence of methicillin-resistant Staphylococcus aureus.
Robinson DA, Enright MC., Antimicrob. Agents Chemother. 47(12), 2003
PMID: 14638503
Robinson DA, Enright MC., Antimicrob. Agents Chemother. 47(12), 2003
PMID: 14638503
Short-Sequence DNA Repeats in Prokaryotic Genomes
van, Microbiology and Molecular Biology Rev 62(), 1998
van, Microbiology and Molecular Biology Rev 62(), 1998
Nucleotide sequence of a variant protein A of Staphylococcus aureus suggests molecular heterogeneity among strains.
Brigido Mde M, Barardi CR, Bonjardin CA, Santos CL, Junqueira ML, Brentani RR., J. Basic Microbiol. 31(5), 1991
PMID: 1813622
Brigido Mde M, Barardi CR, Bonjardin CA, Santos CL, Junqueira ML, Brentani RR., J. Basic Microbiol. 31(5), 1991
PMID: 1813622
National Nosocomial Infections Surveillance (NNIS) System Report, Data Summary from January 1990-May 1999, issued June 1999. A report from the NNIS System.
NNIS System, Gerberding J, Gaynes R, Horan T, Abshire J, Alonso-Echanove J, Edwards J., Am J Infect Control 27(6), 1999
PMID: 10586157
NNIS System, Gerberding J, Gaynes R, Horan T, Abshire J, Alonso-Echanove J, Edwards J., Am J Infect Control 27(6), 1999
PMID: 10586157
Variation of the polymorphic region X of the protein A gene during persistent airway infection of cystic fibrosis patients reflects two independent mechanisms of genetic change in Staphylococcus aureus.
Kahl BC, Mellmann A, Deiwick S, Peters G, Harmsen D., J. Clin. Microbiol. 43(1), 2005
PMID: 15635028
Kahl BC, Mellmann A, Deiwick S, Peters G, Harmsen D., J. Clin. Microbiol. 43(1), 2005
PMID: 15635028
spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation.
Koreen L, Ramaswamy SV, Graviss EA, Naidich S, Musser JM, Kreiswirth BN., J. Clin. Microbiol. 42(2), 2004
PMID: 14766855
Koreen L, Ramaswamy SV, Graviss EA, Naidich S, Musser JM, Kreiswirth BN., J. Clin. Microbiol. 42(2), 2004
PMID: 14766855
High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing.
Le Fleche P, Fabre M, Denoeud F, Koeck JL, Vergnaud G., BMC Microbiol. 2(), 2002
PMID: 12456266
Le Fleche P, Fabre M, Denoeud F, Koeck JL, Vergnaud G., BMC Microbiol. 2(), 2002
PMID: 12456266
Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats.
Frothingham R, Meeker-O'Connell WA., Microbiology (Reading, Engl.) 144 ( Pt 5)(), 1998
PMID: 9611793
Frothingham R, Meeker-O'Connell WA., Microbiology (Reading, Engl.) 144 ( Pt 5)(), 1998
PMID: 9611793
AUTHOR UNKNOWN, 2005
Multilocus Sequence Typing for Characterization of Methicillin-Resistant and Methicillin-Susceptible Clones of
enright, J Clinical Microbiology 38(), 2000
enright, J Clinical Microbiology 38(), 2000
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
QAlign: quality-based multiple alignments with dynamic phylogenetic analysis.
Sammeth M, Rothganger J, Esser W, Albert J, Stoye J, Harmsen D., Bioinformatics 19(12), 2003
PMID: 12912847
Sammeth M, Rothganger J, Esser W, Albert J, Stoye J, Harmsen D., Bioinformatics 19(12), 2003
PMID: 12912847
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 17085848
PubMed | Europe PMC
Suchen in