Evaluation of the color-coding method for searching tandem repeats in prokaryotic genomes

Chem-Bio Informatics Journal

Volumn 4, Issue 4, 2004, Pages 133-141

  Mizuta, Satoshi ^a   Munakata, Hikaru ^a   Aimaiti, Abulimiti ^a   Oosawa, Kenji ^b   Shimizu, Toshio ^a  

^a HIROSAKI UNIVERSITY   (Japan)

^b GUNMA UNIVERSITY   (Japan)

Author keywords

Color coding (CC); Individual variation; Performance evaluation; Tandem repeats; Tandem Repeats Finder (TRF); Visual inspection

Indexed keywords

ALGORITHM; ARTICLE; DEINOCOCCUS RADIODURANS; GENE SEQUENCE; GENOME; HAEMOPHILUS INFLUENZAE; PROKARYOTE; TANDEM REPEAT; YERSINIA PESTIS;

EID: 18244405741     PISSN: 13476297     EISSN: None     Source Type: Journal    
DOI: 10.1273/cbij.4.133     Document Type: Article

References (22)

1. V.B. Sreenu, V. Alevoor, J. Nagarajul, and H.A. Nagarajaram, Nucleic Acids Res., 31, 106-108 (2003).
2. M.V. Katti, P.K. Ranjekar, and V.S. Gupta, Mol. Biol. Evol., 18, 1161-1167 (2001).
3. B. Borstnik and D. Pumpernik, Genome Res., 12, 909-915 (2002).
4. G. Ahaz, E.P.C. Rocha, P. Netter, and E. Coissac, Nucleic Acids Res., 30, 2987-2994 (2002).
5. E.P.C. Rocha and A. Blanchard, Nucleic Acids Res., 30, 2031-2042 (2002).
6. P.L. Flèche, Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud, V. Ramisse, P. Sylvestre, G. Benson, F. Ramisse, and G. Vergnaud, BMC Microbiology, 1: 2, (2001)
7. H.H. Kazazian Jr., Science, 303, 1626-1632 (2004).
8. S.A. Teichmann, S.C.G. Rison, J.M. Thornton, M. Riley, J. Gough, and C. Chothia, J. Mol. Biol., 311, 693-708 (2001).
9. C. Vogel, C. Berzuini, M. Bashton, J. Gough, and S.A. Teichmann, J. Mol. Biol., 336, 809-823 (2004).
10. T. Shimizu, H. Mitsuke, K. Noto, and M. Arai, J. Mol. Biol., 339, 1-15 (2004).
11. G. Benson, Nucleic Acids Res., 27, 573-580 (1999).
12. T.A. Castelo, W. Martins, R.G. Gao, Bioinformatics, 18, 634-636 (2002).
13. C. Abajian, Sputnik, http://avajian.net/sputnik/ (1994).
14. S. Kurtz and C. Schleiermacher, Bioinformatics, 15, 426-427 (1999).
15. A. Lefebvre, T. Lecroq, H. Dauchel, and J. Alexandre, Bioinformatics, 19, 319-326 (2003).
16. T. Yoshida, N. Obata, and K. Oosawa, J. Mol. Biol., 298, 343-349 (2000).
17. W.R. Taylor, Protein Eng., 10, 743-746 (1997).
18. J. Parkhill, B.W. Wren, N.R. Thomson, R.W. Titball, M.T. Holden, M.B. Prentice, M. Sebaihia, K.D. James, C. Churcher, K.L. Mungall et al., Nature, 413, 523-527 (2001).
19. R.D. Fleischmann, M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness, A.R. Kerlavage, C.J. Bult, J.F. Tomb, B.A. Dougherty, J.M. Merrick et al., Science, 269, 496-512 (1995).
20. O. White, J.A. Eisen, J.F. Heidelberg, E.K. Hickey, J.D. Peterson, R.J. Dodson, D.H. Haft, M.L. Gwinn, W.C. Nelson, D.L. Richardson et al., Science, 286, 1571-1577 (1999).
21. D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, and D.L. Wheeler, Nucleic Acids Res., 32, D23-D26 (2004).
22. S.J. Humphray, K. Oliver, A.R. Hunt, R.W. Plumb, J.E. Loveland, K.L. Howe, T.D. Andrews, S. Searle, S.E. Hunt, C.E. Scott et al., Nature, 429, 369-374 (2004).