Multidotter: Dot-matrix program for multiple sequences

Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05

Volumn , Issue , 2005, Pages 25-30

  Nozaki, Y ^a   Macgregor, A ^a   Smith, C ^a   Hunter, A ^a   Bellgard, M ^a  

^a MURDOCH UNIVERSITY   (Australia)

Author keywords

Comparative genomic analysis; Dot matrix analysis; Sequence comparisons

Indexed keywords

COMPARATIVE GENOMIC ANALYSIS; CONSERVED REGIONS; DOT-MATRIX ANALYSIS; GENOME SEQUENCES; INPUT SEQUENCES; MATRIX ALGORITHMS; MATRIX PAIRS; MATRIXES; MULTIPLE SEQUENCES; SEQUENCE COMPARISONS; TWO DIMENSIONAL IMAGES; WHOLE GENOME SEQUENCING;

NUCLEIC ACIDS;

EID: 60749102727     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. Enard W. and Paabo S. "Comparative primate genomics." Annu Rev Genomics Hum Genet 5: 351-378, 2004.
2. Hardison R. C. "Comparative genomics." PLoS Biol 1(2): E58, Nov 2003.
3. Miller W., Makova K. D., Nekrutenko A., and Hardison R. C. "Comparative genomics." Annu Rev Genomics Hum Genet 5: 15-56, 2004.
4. Thomas J. W., Touchman J. W., Blakesley R. W., Bouffard G. G., Beckstrom-Sternberg S. M., Margulies E. H., Blanchette M., Siepel A. C., Thomas P. J., McDowell J. C., Maskeri B., Hansen N. F., Schwartz M. S., Weber R. J., Kent W. J., Karolchik D., Bruen T. C., Bevan R., Cutler D. J., Schwartz S., Elnitski L., Idol J. R., Prasad A. B., Lee-Lin S. Q., Maduro V. V., Summers T. J., Portnoy M. E., Dietrich N. L., Akhter N., Ayele K., Benjamin B., Cariaga K., Brinkley C. P., Brooks S. Y., Granite S., Guan X., Gupta J., Haghighi P., Ho S. L., Huang M. C., Karlins E., Laric P. L., Legaspi R., Lim M. J., Maduro Q. L., Masiello C. A., Mastrian S. D., McCloskey J. C., Pearson R., Stantripop S., Tiongson E. E., Tran J. T., Tsurgeon C., Vogt J. L., Walker M. A., Wetherby K. D., Wiggins L. S., Young A. C., Zhang L. H., Osoegawa K., Zhu B., Zhao B., Shu C. L., De Jong P. J., Lawrence C. E., Smit A. F., Chakravarti A., Haussler D., Green P., Miller W. and Green E. D. "Comparative analyses of multi-species sequences from targeted genomic regions." Nature 424(6950): 788-793, Aug 2003.
5. Kulski J. K., Shiina T., Anzai T., Kohara S. and Inoko H. "Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man." Immunol Rev, 190: 95-122, Dec 2002.
6. Fitch W. M. "Locating gaps in amino acid sequences to optimize the homology between two proteins." Biochem Genet 3(2): 99-108, Apr 1969.
7. Gibbs A. J. and McIntyre G. A. "The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences." Eur J Biochem 16(1): 1-11, Sep 1970.
8. Sonnhammer E. L. and Durbin R. "A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis." Gene 167(1-2): GC1-GC10, Dec 1995.
9. Rice P., Longden I. and Bleasby A. "EMBOSS: the European Molecular Biology Open Software Suite." Trends Genet 16(6): 276-277, Jun 2000.
10. Huang Y. and Zhang L. "Rapid and sensitive dot-matrix methods for genome analysis." Bioinformatics 20(4): 460-466, Mar 2004.
11. Lipman D. J. and Pearson W. R. "Rapid and sensitive protein similarity searches." Science 227(4693): 1435-1441, Mar 1985.
12. Lewin, B. "Genes VII." Oxford University Press, 1999.
13. Appels R., Francki M. and Chibbar R. "Advances in cereal functional genomics." Funct Integr Genomics 3(1-2): 1-24, Mar 2003.
14. Dubcovsky J., Ramakrishna W., SanMiguel P. J., Busso C. S., Yan L., Shiloff B. A. and Bennetzen J. L. "Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes." Plant Physiol 125(3): 1342-1353, Mar 2001.
15. Lefebvre J. F., El-Mabrouk N., Tillier E. and Sankoff D. "Detection and validation of single gene inversions." Bioinformatics 19(Suppl 1): i190-i196, 2003.
16. Pevzner P. and Tesler G. "Genome rearrangements in mammalian evolution: lessons from human and mouse genomes." Genome Res 13(1): 37-45, Jan 2003.
17. Pevzner P. and Tesler G. "Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution." Proc Natl Acad Sci USA. 100(13): 7672-7677, Jun 2003.