An Exact Formula for the Number of Alignments between Two DNA Sequences

DNA Sequence - Journal of DNA Sequencing and Mapping

Volumn 14, Issue 6, 2003, Pages 427-430

  Torres, Angela ^a   Cabada, Alberto ^b   Nieto, Juan J ^b  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^b UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

Alignment; Difference equation; DNA sequence; Exact formula

Indexed keywords

DNA;

ARTICLE; DNA SEQUENCE; GENE SEQUENCE; GENOME; MATHEMATICAL ANALYSIS; MATHEMATICS; NUCLEOTIDE SEQUENCE;

ALGORITHMS; BASE SEQUENCE; MODELS, THEORETICAL; SEQUENCE ALIGNMENT;

EID: 0345098558     PISSN: 10425179     EISSN: None     Source Type: Journal    
DOI: 10.1080/10425170310001617894     Document Type: Article

References (18)

1. Altschul, S.F., Bundschuh, R., Olsen, R. and Hwa, T. (2001) "The estimation of statistical parameters for local alignment score distributions", Nucleic Acid Research 29, 351-361.
2. Forster, M., Heath, A. and Afzal, M. (1999) "Application of distance geometry to 3D visualization of sequence relationships", Bioinformatics 15, 89-90.
3. Gusev, V.D., Nemytikova, L.A. and Chuzhanova, N.A. (1999) "On the complexity measures of genetic sequences", Bioinformatics 15, 994-999.
4. Jamshidi, N., Edwards, J.S., Fahland, T., Church, G.M. and Palsson, B.O. (2001) "Dynamic simulation of the human red blood cell metabolic network", Bioinformatics 17, 286-287.
5. Jiang, T., Lin, G., Ma, B. and Zhang, K. (2002) "A general edit distance between RNA structures", Journal of Computational Biology 9, 371-388.
6. Kelley, W.G. and Peterson, A.C. (2001) Difference Equations. An Introduction with Applications (Academic Press, San Diego).
7. Lange, K. (2002) Mathematical and Statistical Methods for Genetic Analysis (Springer-Verlag, New York).
8. Lesk, A.M. (2002) Introduction to Bioinformatics (Oxford University Press, Oxford).
9. Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P. and Zhang, H. (2001) "An information-based sequence distance and its application to whole mitochondrial phylogeny", Bioinformatics 17, 149-154.
10. Liben-Nowell, D. (2001) "On the structure of syntenic distance", Journal of Computational Biology 8, 53-67.
11. Morgenstern, B. (2002) "A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences", Applied Mathematics Letters 15, 11-16.
12. Nieto, J.J., Torres, A. and Vázquez-Trasande, M.M. (2003) "A metric space to study differences between polynucleotides", Applied Mathematics Letters, in press.
13. Nowak, M.A. and May, R.M. (2000) Virus Dynamics (Oxford University Press, Oxford).
14. Paun, Gh., Rozenberg, G. and Salomaa, A. (1998) DNA Computing: New Computing Paradigms (Springer-Verlag, Berlin).
15. Percus, J. (2002) Mathematics of Genome Analysis (Cambridge University Press, Cambridge).
16. Sadovsky, M.G. (2003) "The method to compare nucleotide sequences based on the minimum entropy principle", Bulletin of Mathematical Biology 65, 309-322.
17. Tang, B. (2000) "Evaluation of some DNA cloning strategies", Computers and Mathematics with Applications 39, 43-48.
18. Torres, A. and Nieto, J.J. (2003) "The fuzzy polynucleotide space: basic properties", Bioinformatics 19, 587-592.