Advertisement

INVERTER: INtegrated Variable numbER Tandem rEpeat findeR

  • Adrianto Wirawan
  • Chee Keong Kwoh
  • Li Yang Hsu
  • Tse Hsien Koh
Part of the Communications in Computer and Information Science book series (CCIS, volume 115)

Abstract

A tandem repeat in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing (DNA fingerprinting), sequence homology and population studies. Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence. In this paper, we present INVERTER, a de novo tandem repeat finder without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool. INVERTER is implemented in Java and has a built-in user-friendly Graphical User Interface. A standalone version of the program can be downloaded from http://bmserver.sce.ntu.edu.sg/INVERTER . Comparison search result of INVERTER with an existing software tool is presented. The use of INVERTER will assist biologists in discovering new ways of understanding both the structure and function of DNA and protein.

Keywords

Variable Number Tandem Repeat exact match search non-exact match search data visualization 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Collins, F.S., Morgan, M., Patrinos, A.: The Human Genome Project: Lessons from large-scale biology. Science 300, 286–290 (2003)CrossRefPubMedGoogle Scholar
  2. 2.
    Kannan, S.K., Myers, E.W.: An algorithm for locating nonoverlapping regions of maximum alignment score. SIAM Journal on Computing 25, 648–662 (1996)CrossRefGoogle Scholar
  3. 3.
    Verkerk, A.J.M.H., Pieretti, M., Sutcliffe, J.S., Fu, Y.H., Kuhl, D.P.A., Pizzuti, A., Reiner, O., Richards, S., Victoria, M.F., Zhang, F., Eussen, B.E., Van Ommen, G.J.B., Blonden, L.A.J., Riggins, G.J., Chastain, J.L., Kunst, C.B., Galjaard, H., Caskey, C.T., Nelson, D.L., Oostra, B.A., Warren, S.T.: Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell 65, 905–914 (1991)CrossRefPubMedGoogle Scholar
  4. 4.
    Fu, Y.H., Pizzuti, A., Fenwick Jr, R.G., King, J., Rajnarayan, S., Dunne, P.W., Dubel, J., Nasser, G.A., Ashizawa, T., De Jong, P., Wieringa, B., Korneluk, R., Perryman, M.B., Epstein, H.F., Caskey, C.T.: An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 255, 1256–1258 (1992)CrossRefPubMedGoogle Scholar
  5. 5.
    MacDonald, M.E., Ambrose, C.M., Duyao, M.P., Myers, R.H., Lin, C., Srinidhi, L., Barnes, G., Taylor, S.A., James, M., Groot, N., MacFarlane, H., Jenkins, B., Anderson, M.A., Wexler, N.S., Gusella, J.F., Bates, G.P., Baxendale, S., Hummerich, H., Kirby, S.: A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell 72, 971–983 (1993)CrossRefGoogle Scholar
  6. 6.
    La Spada, A.R., Wilson, E.M., Lubahn, D.B., Harding, A.E., Fischbeck, K.H.: Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy. Nature 352, 77–79 (1991)CrossRefPubMedGoogle Scholar
  7. 7.
    Campuzano, V., Montermini, L., Molto, M.D., Pianese, L., Cossee, M., Cavalcanti, F., Monros, E., Rodius, F., Duclos, F., Monticelli, A., Zara, F., Canizares, J., Koutnikova, H., Bidichandani, S.I., Gellera, C., Brice, A., Trouillas, P., De Michele, G., Filla, A., De Frutos, R., Palau, F., Patel, P.I., Di Donato, S., Mandel, J.L., Cocozza, S., Koenig, M., Pandolfo, M.: Friedreich’s ataxia: Autosomal recessive disease caused by an intronic GAA triplet repeat expansion. Science 271, 1423–1427 (1996)CrossRefPubMedGoogle Scholar
  8. 8.
    Mirkin, S.M.: DNA structures, repeat expansions and human hereditary disorders. Current Opinion in Structural Biology 16, 351–358 (2006)CrossRefPubMedGoogle Scholar
  9. 9.
    Usdin, K.: The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases. Genome Research 18, 1011–1019 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Jeffreys, A.J.: DNA typing: Approaches and applications. Journal of the Forensic Science Society 33, 204–211 (1993)CrossRefPubMedGoogle Scholar
  11. 11.
    Bruford, M.W., Wayne, R.K.: Microsatellites and their application to population genetic studies. Current Opinion in Genetics and Development 3, 939–943 (1993)CrossRefPubMedGoogle Scholar
  12. 12.
    Spong, G., Hellborg, L.: A near-extinction event in lynx: Do microsatellite data tell the tale? Conservation Ecology 6 (2002)Google Scholar
  13. 13.
    Benson, G.: Sequence alignment with tandem duplication. In: Conference Sequence alignment with tandem duplication, pp. 27–36 (1997)Google Scholar
  14. 14.
    Benson, G.: Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research 27, 573–580 (1999)CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Kolpakov, R., Bana, G., Kucherov, G.: mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Research 31, 3672–3678 (2003)CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Wexler, Y., Yakhini, Z., Kashi, Y., Geiger, D.: Finding approximate tandem repeats in genomic sequences. Journal of Computational Biology 12, 928–942 (2005)CrossRefPubMedGoogle Scholar
  17. 17.
    Parisi, V., De Fonzo, V., Aluffi-Pentini, F.: STRING: Finding tandem repeats in DNA sequences. Bioinformatics 19, 1733–1738 (2003)CrossRefPubMedGoogle Scholar
  18. 18.
    Jorda, J., Kajava, A.V.: T-REKS: Identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics 25, 2632–2638 (2009)CrossRefPubMedGoogle Scholar
  19. 19.
    Turnpenny, P., Ellard, S.: Emery’s Elements of Medical Genetics. Elsevier, London (2005)Google Scholar
  20. 20.
    Jeffreys, A.J., Wilson, V., Thein, S.L.: Hypervariable ’minisatellite’ regions in human DNA. Nature 314, 67–73 (1985)CrossRefPubMedGoogle Scholar
  21. 21.
    Merkel, A., Gemmell, N.: Detecting short tandem repeats from genome data: Opening the software black box. Briefings in Bioinformatics 9, 355–366 (2008)CrossRefPubMedGoogle Scholar
  22. 22.
    MacQueen, J.B.: Some Methods for Classification and Analysis of MultiVariate Observations. In: Cam, L.M.L., Neyman, J. (eds.) Proc. of the fifth Berkeley Symposium on Mathematical Statistics and Probability, vol. 1, pp. 281–297. University of California Press, Berkeley (1967)Google Scholar
  23. 23.
    Sanchez, J., Lopez-Villasenor, I.: A simple model to explain three-base periodicity in coding DNA. FEBS Lett. 580, 6413–6422 (2006)CrossRefPubMedGoogle Scholar
  24. 24.
    Lopez-Villasenor, I., Jose, M., Sanchez, J.: Three-base periodicity patterns and self-similarity in whole bacterial chromosomes. Biochem. Biophys. Res. Commun. 325, 467–478 (2004)CrossRefPubMedGoogle Scholar
  25. 25.
    Schieg, P., Herzel, H.: Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA. J. Mol. Biol. 343, 891–901 (2004)CrossRefPubMedGoogle Scholar
  26. 26.
    Turton, J.F., Matos, J., Kaufmann, M.E., Pitt, T.L.: Variable number tandem repeat loci providing discrimination within widespread genotypes of acinetobacter baumannii. European Journal of Clinical Microbiology and Infectious Diseases 28, 499–507 (2009)CrossRefPubMedGoogle Scholar
  27. 27.
    Wareham, D.W., Bean, D.C., Khanna, P., Hennessy, E.M., Krahe, D., Ely, A., Millar, M.: Bloodstream infection due to Acinetobacter spp: Epidemiology, risk factors and impact of multi-drug resistance. European Journal of Clinical Microbiology and Infectious Diseases 27, 607–612 (2008)CrossRefPubMedGoogle Scholar
  28. 28.
    Dijkshoorn, L., Nemec, A., Seifert, H.: An increasing threat in hospitals: Multidrug-resistant Acinetobacter baumannii. Nature Reviews Microbiology 5, 939–951 (2007)CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Adrianto Wirawan
    • 1
    • 2
  • Chee Keong Kwoh
    • 1
  • Li Yang Hsu
    • 2
  • Tse Hsien Koh
    • 2
  1. 1.School of Computer EngineeringNanyang Technological UniversitySingapore
  2. 2.Department of Medicine, Yong Loo Lin School of MedicineNational University of SingaporeSingapore

Personalised recommendations