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Comparing Tandem Repeats with Duplications and Excisions of Variable Degree
October-December 2006 (vol. 3 no. 4)
pp. 395-407
ASCII Text
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Michael Sammeth, Jens Stoye, "Comparing Tandem Repeats with Duplications and Excisions of Variable Degree," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 395-407, October-December, 2006.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2006.46,
author = {Michael Sammeth and Jens Stoye},
title = {Comparing Tandem Repeats with Duplications and Excisions of Variable Degree},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {3},
number = {4},
issn = {1545-5963},
year = {2006},
pages = {395-407},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2006.46},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Comparing Tandem Repeats with Duplications and Excisions of Variable Degree
IS - 4
SN - 1545-5963
SP395
EP407
EPD - 395-407
A1 - Michael Sammeth,
A1 - Jens Stoye,
PY - 2006
KW - Sequence comparison
KW - tandem repeats
KW - variable number of tandem repeats
KW - repeat duplication history
KW - pairwise alignment
KW - dynamic programming.
VL - 3
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
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.

[1] P.L. Flèche, Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud, V. Ramisse, P. Sylvestre, F. Ramisse, and G. Vergnaud, “A Tandem Repeats Database for Bacterial Genomes: Application to the Genotyping of Yersinia Pestis and Bacillus Anthracis,” BMC Microbiology, vol. 1, p. 2, 2001.
[2] R. Fronthingham and W. Meeker-O'Connell, “Genetic Diversity in the Mycobacterium Tuberculosis Complex Based on Variable Numbers of Tandem DNA Repeats,” Microbiology, vol. 144, pp.1189-1196, 1998.
[3] P.L. Flèche, M. Fabre, F. Denoeud, J.-L. Koeck, and G. Vergnaud, “High Resolution, On-Line Identification of Strains from the Mycobacterium Tuberculosis Complex Based on Tandem Repeat Typing,” BMC Microbiology, vol. 2, p. 37, 2002.
[4] L. Koreen, S.V. Ramaswamy, E.A. Graviss, S. Naidich, J.M. Musser, and B.N. Kreiswirth, “Spa Typing Method for Discriminating Among Staphylococcus Aureus Isolates: Implications for Use of a Single Marker to Detect Genetic Micro- and Macrovariation,” J. Clinical Microbiology, vol. 47, pp. 792-799, 2004.
[5] B. Kahl, A. Mellmann, S. Deiwick, G. Peters, and D. Harmsen, “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,” J. Clinical Microbiology, vol. 43, pp. 502-505, 2005.
[6] N.N.I.S. System, “National Nocosomial Infections Surveillance (NNIS) System Report, Data Summary from January 1990-May 1999,” Am. J. Infectious Control, vol. 27, pp. 520-532, 1999.
[7] M. de Macedo Brigido, C.R.M. Barardi, C.A. Bonjardin, C.L.S. Santos, M. de Lourdes Junqueira, and R.R. Brentani, “Nucleotide Sequence of a Variant Protein A of Staphylococcus Aureus Suggests Molecular Heterogeneity among Strains,” J. Basic Microbiology, vol. 31, pp. 337-345, 1991.
[8] A. van Belkum, S. Scherer, L. van Alphen, and H. Verbrugh, “Short-Sequence DNA Repeats in Prokaryotic Genomes,” Microbiology and Molecular Biology Rev., vol. 62, pp. 275-293, 1998.
[9] D.A. Robinson and M.C. Enright, “Evolutionary Models of the Emerge of Methicillin-Resistant Staphylococcus Aureus,” Antimicrobial Agents Chemotherapy, vol. 47, pp. 3926-3934, 2003.
[10] R. Groult, M. Léonard, and L. Mouchard, “A Linear Algorithm for the Detection of Evolutive Tandem Repeats,” Proc. Prague Stringology Conf., 2003.
[11] D. Gusfield and J. Stoye, “Linear Time Algorithms for Finding and Representing All the Tandem Repeats in a String,” J. Computer Systems Science, vol. 69, no. 4, pp. 525-546, 2004.
[12] G. Benson, “Sequence Alignment with Tandem Duplication,” J.Computational Biology, vol. 4, pp. 351-367, 1997.
[13] S. Bèrard and E. Rivals, “Comparison of Minisatellites,” J.Computational Biology, vol. 10, pp. 357-372, 2003.
[14] B. Behzadi and J.-M. Steyaert, “The Minisatellite Transformational Problem Revisted,” Proc. Workshop Algorithms in Bioinformatics (WABI '04), pp. 310-320, 2004.
[15] G. Benson and L. Dong, “Reconstructing the Duplication History of a Tandem Repeat,” Proc. Int'l Conf. Intelligent Systems for Microbiology (ISMB '99), pp. 44-53, 1999.
[16] D. Jaitly, P. Kearney, G.-H. Lin, and B. Ma, “Reconstructing the Duplication History of Tandemly Repeated Genes,” J. Computer Systems Science, vol. 65, pp. 494-507, 2002.
[17] O. Elemento, O. Gascuel, and M.-P. Lefranc, “Reconstructing the Duplication History of Tandemly Repeated Genes,” Molecular Biology Evolution, vol. 19, pp. 278-288, 2002.
[18] D. Bertrand and O. Gascuel, “Topological Rearrangements and Local Search Method for Tandem Duplication Trees,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 1-13, Jan-Mar. 2005.
[19] M. Sammeth, T. Weniger, D. Harmsen, and J. Stoye, “Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI),” Proc. Fifth Int'l Workshop Algorithms in Bioinformatics (WABI '05), pp. 276-290, 2005.
[20] E. Rivals, “A Survey on Algorithmic Aspects of Tandem Repeats Evolution,” Int'l J. Foundations of Computer Science, vol. 15, pp. 225-257, 2004.
[21] M. Waterman, Introduction to Computational Biology: Maps, Sequences, and Genomes. CRC Press, 1995.
[22] M. Sammeth, J. Rothgänger, W. Esser, J. Albert, J. Stoye, and D. Harmsen, “Qalign: Quality Based Multiple Alignments with Dynamic Phylogenetic Analysis,” Bioinformatics, vol. 19, pp.1592-1593, 2003.
[23] W. Fitch, “Phylogenies Constrained by Cross-Over Process as Illustrated by Human Hemoglobins in a Thirteen-Cycle, Eleven Amino-Acid Repeat in Human Apolipoprotein A-I,” Genetics, vol. 86, pp. 623-644, 1977.
[24] Ridom nomenclature server, http://www.ridom.de/spaservernomenclature.shtml , 2005.
[25] M. Enright, N. Day, C. Davies, S. Peacock, and B. Spratt, “Multilocus Sequence Typing for Characterization of Methicillin-Resistant and Methicillin-Susceptible Clones of Staphylococcus Aureus,” J. Clinical Microbiology, vol. 38, pp. 1008-1015, 2000.

Index Terms:
Sequence comparison, tandem repeats, variable number of tandem repeats, repeat duplication history, pairwise alignment, dynamic programming.
Citation:
Michael Sammeth, Jens Stoye, "Comparing Tandem Repeats with Duplications and Excisions of Variable Degree," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 395-407, Oct.-Dec. 2006, doi:10.1109/TCBB.2006.46
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