Aligning coding DNA in the presence of frame-shift errors

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 1264, Issue , 1997, Pages 180-190

  Arvestad, Lars ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DNA; DNA SEQUENCES; PATTERN MATCHING;

OBJECTIVE FUNCTIONS;

CODING ERRORS;

EID: 33845801168     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-63220-4_59     Document Type: Conference Paper

References (15)

1. K.-M. Chao. Computing all suboptimal alignments in linear space. In 5th Symposium on Combinatorial Pattern Matching, pages 31-42. Springer-Verlag LNCS 807, 1994.
2. M. O. Dayhoff, R. M. Schwartz, and B. C. Orcott. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure, 5:345-352, 1978. National Biomedical Research Foundation, Silver Spring, Maryland, USA.
3. O. Gotoh. An improved algorithm for matching biological sequences. Journal of Molecular Biology, 162:705-708, 1982.
4. X. Guan and E. C. Uberbacher. Alignments of DNA and protein sequences congaining frameshift errors. Comp. Appl. Bio. Sci., 12(1):31-40, 1996.
5. J. Hein. An algorithm combining DNA and protein alignment. Journal of Theoretical Biology, 167:169-174, 1994.
6. S. Henikoff and J. G. Henikoff. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad.Sci., 89:10915-10919, 1992.
7. D. S. Hirschberg. A linear space algorithm for computing longest common subsequences. Communications of the ACM, 18:341-343, 1975.
8. L. J. Knecht. Alignment and Analysis of Genes Coding for Proteins. PhD thesis, Swiss Federal Institute of Technology, 1996.
9. T. Leitner. Personal communication. Until recently at the Department of Biochemistry, Royal Institute of Technology, Stockholm, now at Los Alamos National Laboratory, USA, Theoretical Biology and Biophysics Group.
10. E. W. Myers and W. Miller. Optimal alignments in linear space. Comp. Appl. Bio. Sci., 4(1):11-17, 1988.
11. H. Peltola, H. Söderlund, and E. Ukkonen. Algorithms for the search of amino acid patterns in nucleic acid sequences. Nuclear Acids Research, 14(1):99-107, 1986.
12. D. Sankoff and J. Kruskal. Time warps, string edits, and macromolecules: The theory and practice of sequence comparison. Addison-Wesley, 1983.
13. P. H. Sellers. On the theory and computation of evolutionary distances. SIAM Journal on Applied Mathematics, 26:787, 1974.
14. D. J. States and D. Botstein. Molecular sequence accuracy and the analysis of protein coding regions. Proc. Natl. Acad.Sci., 88:5518-5522, July 1991.
15. M. S. Waterman. Introduction to computational biology: Maps, sequences and genomes. Chapman & Hall, 1995.