The generalised κ-truncated suffix tree for time-and space-efficient searches in multiple DNA or protein sequences

International Journal of Bioinformatics Research and Applications

Volumn 4, Issue 1, 2008, Pages 81-95

  Schulz, Marcel H ^a,b   Bauer, Sebastian ^a   Robinson, Peter N ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b INTERNATIONAL MAX PLANCK RESEARCH SCHOOL FOR COMPUTATIONAL BIOLOGY AND SCIENTIFIC COMPUTING   (Germany)

Author keywords

Bioinformatics; Biological sequence analysis; Suffix array; Suffix tree

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; DNA SEQUENCE; GENOMICS; SEQUENCE ANALYSIS; AUTOMATED PATTERN RECOGNITION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

ALGORITHMS; AMINO ACID SEQUENCE; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

EID: 39449128278     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2008.017165     Document Type: Article

References (19)

1. Abouelhoda, M.I., Kurtz, S. and Ohlebusch, E. (2004) 'Replacing suffix trees with enhanced suffix arrays', Journal of Discrete Algorithms, Vol. 2, pp.53-86.
2. Allali, J. and Sagot, M-F. (2004) The at Most k-Deep Factor Tree, Technical Report No. 2004-2003, Institut Gaspard Monge, Université de Marne la Vallée.
3. Carvalho, A.M., Oliveira, A.L., Freitas, A.T. and Sagot, M-F. (2004) 'A parallel algorithm for the extraction of structured motifs', SAC '04: Proceedings of the 2004 ACM Symposium on Applied Computing, Nicosia, Cyprus, pp.147-153.
4. Giegerich, R. and Kurtz, S. (1995) 'A comparison of imperative and purely functional suffix tree constructions', ESOP'94: Selected papers of ESOP'94, the 5th European symposium on Programming, Edinburgh, Scotland, pp.187-218.
5. Giegerich, R., Kurtz, S. and Stoye, J. (2003) 'Efficient implementation of lazy suffix trees software', Practice and Experience, Vol. 33, pp.1035-1049.
6. Gusfield, D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, New York, NY, USA.
7. Kärkkäinen, J. and Sanders, P. (2003) 'Simple linear work suffix array construction', Proc. 30th International Conference on Automata, Languages and Programming, The Netherlands, pp.943-955.
8. Kim, D.K., Sim, J.S., Park, H. and Park, K. (2003) 'Linear-time construction of suffix arrays', Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching (CPM'03), Lecture Notes in Computer Science, Vol. 2676, pp.186-199.
9. Ko, P. and Aluru, S. (2003) 'Space efficient linear time construction of suffix arrays', Lecture Notes in Computer Science, Vol. 2676, pp.200-210.
10. Kurtz, S. (1999) 'Reducing the space requirement of suffix trees', Softw. Pract. Exper., Vol. 29, pp.1149-1171.
11. Leslie, C., Eskin, E. and Noble, W.S. (2002) 'The spectrum kernel: a string kernel for SVM protein classification', Pac. Symp. Biocomput., pp.564-575.
12. Manber, U. and Myers, G. (1990) 'Suffix arrays: a new method for on-line string searches', SODA'90: Proceedings of the First AnnualACM-SIAMSymposium on Discrete Algorithms, San Francisco, California, USA, pp.319-327.
13. Manzini, G. and Ferragina, P. (2004) 'Engineering a lightweight suffix array construction algorithm', Algorithmica, Vol. 40, pp.33-50.
14. McCreight, E.M. (1976) 'A space-economical suffix tree construction algorithm', J. ACM, Vol. 23, pp.262-272.
15. Mootha, V.K., Handschin, C., Arlow, D., Xie, X., St. Pierre, J., Sihag, S., Yang, W., Altshuler, D., Puigserver, P., Patterson, N., Willy, P.J., Schulman, I.G., Heyman, R.A., Lander, E.S. and Spiegelman, B.M. (2004) 'Errα and Gabpa/b specify PGC-1α-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle', Proc. Natl. Acad. Sci. USA, Vol. 101, pp.6570-6575.
16. Na, J.C., Apostolico, A., Iliopoulos, C.S. and Park, K. (2003) 'Truncated suffix trees and their application to data compression', Theor. Comput. Sci., Vol. 304, pp.87-101.
17. Puglisi, S.J., Smyth, W.F. and Turpin, A. (2005) 'The performance of linear time suffix sorting algorithms', Data Compression Conference (DCC'05), Snowbird, Utah, USA, pp.358-367.
18. Ukkonen, E. (1995) 'On-line construction of suffix trees', Algorithmica, Vol. 14, pp.249-260.
19. http://gsuffix.sourceforge.net