REPuter: the manifold applications of repeat analysis on a genomic scale

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
Nucleic Acids Research 29(22): 4633-4642.

Download
OA
Journal Article | Published | English
Author
; ; ; ; ;
Abstract
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research. 2001;29(22):4633-4642.
Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., & Giegerich, R. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22), 4633-4642.
Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., and Giegerich, R. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29, 4633-4642.
Kurtz, S., et al., 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22), p 4633-4642.
S. Kurtz, et al., “REPuter: the manifold applications of repeat analysis on a genomic scale”, Nucleic Acids Research, vol. 29, 2001, pp. 4633-4642.
Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R.: REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research. 29, 4633-4642 (2001).
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. “REPuter: the manifold applications of repeat analysis on a genomic scale”. Nucleic Acids Research 29.22 (2001): 4633-4642.
Main File(s)
File Name
Access Level
OA Open Access

This data publication is cited in the following publications:
This publication cites the following data publications:

264 Citations in Europe PMC

Data provided by Europe PubMed Central.

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus.
Lei W, Ni D, Wang Y, Shao J, Wang X, Yang D, Wang J, Chen H, Liu C., Sci Rep 6(), 2016
PMID: 26899134
RECA plays a dual role in the maintenance of chloroplast genome stability in Physcomitrella patens.
Odahara M, Inouye T, Nishimura Y, Sekine Y., Plant J. 84(3), 2015
PMID: 26340426
Repetitive genomic sequences as a substrate for homologous integration in the Rhizopus oryzae genome.
Yuzbashev TV, Larina AS, Vybornaya TV, Yuzbasheva EY, Gvilava IT, Sineoky SP., Fungal Biol 119(6), 2015
PMID: 25986546
Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring.
Wang H, Yu Y, Liu T, Pan Y, Yan S, Wang Y., Springerplus 4(), 2015
PMID: 25918685
Detection of dispersed short tandem repeats using reversible jump Markov chain Monte Carlo.
Liang T, Fan X, Li Q, Li SY., Nucleic Acids Res. 40(19), 2012
PMID: 22753023
Efficient maximal repeat finding using the burrows-wheeler transform and wavelet tree.
Kulekci MO, Vitter JS, Xu B., IEEE/ACM Trans Comput Biol Bioinform 9(2), 2012
PMID: 21968959
Comparative analysis of iol clusters in Lactobacillus casei strains
Zhang WY, Sun ZH, Yu DL, Airideng C, Chen W, Meng H, Zhang HP., World J. Microbiol. Biotechnol. 26(11), 2010
PMID: IND44437107
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs.
Dezulian T, Schaefer M, Wiese R, Weigel D, Huson DH., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845036

25 References

Data provided by Europe PubMed Central.

Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium., Nature 409(6822), 2001
PMID: 11237011
Short-sequence DNA repeats in prokaryotic genomes.
van Belkum A, Scherer S, van Alphen L, Verbrugh H., Microbiol. Mol. Biol. Rev. 62(2), 1998
PMID: 9618442

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
The REPRO server: finding protein internal sequence repeats through the Web.
George RA, Heringa J., Trends Biochem. Sci. 25(10), 2000
PMID: 11203383

AUTHOR UNKNOWN, 0
Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982

AUTHOR UNKNOWN, 0
The complete genome sequence of Escherichia coli K-12.
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y., Science 277(5331), 1997
PMID: 9278503
Alignment of whole genomes.
Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL., Nucleic Acids Res. 27(11), 1999
PMID: 10325427
REPuter: fast computation of maximal repeats in complete genomes.
Kurtz S, Schleiermacher C., Bioinformatics 15(5), 1999
PMID: 10366664

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
A chromosomal deletion map of human malformations.
Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D., Am. J. Hum. Genet. 63(4), 1998
PMID: 9758599
Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome.
Edelmann L, Pandita RK, Morrow BE., Am. J. Hum. Genet. 64(4), 1999
PMID: 10090893
Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis.
Shaikh TH, Kurahashi H, Saitta SC, O'Hare AM, Hu P, Roe BA, Driscoll DA, McDonald-McGinn DM, Zackai EH, Budarf ML, Emanuel BS., Hum. Mol. Genet. 9(4), 2000
PMID: 10699172
Prediction of complete gene structures in human genomic DNA.
Burge C, Karlin S., J. Mol. Biol. 268(1), 1997
PMID: 9149143
Complementary DNA sequencing: expressed sequence tags and human genome project.
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF., Science 252(5013), 1991
PMID: 2047873

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 11713313
PubMed | Europe PMC

Search this title in

Google Scholar