Efficient and scalable indexing techniques for biological sequence data

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

Volumn 4414 LNBI, Issue , 2007, Pages 464-479

  Halachev, Mihail ^a   Shiri, Nematollaah ^a   Thamildurai, Anand ^a  

^a Gina Cody School of Engineering and Computer Science   (Canada)

Author keywords

Biological databases; Indexing; Sequences; Suffix trees

Indexed keywords

ALGORITHMS; DATA REDUCTION; DATA STORAGE EQUIPMENT; TREES (MATHEMATICS);

BIOLOGICAL DATABASES; SEQUENCES; SUFFIX ARRAYS (SA); SUFFIX TREES;

INDEXING (OF INFORMATION);

EID: 34548101752     PISSN: 03029743     EISSN: 16113349     Source Type: Conference Proceeding    
DOI: 10.1007/978-3-540-71233-6_36     Document Type: Conference Paper

References (32)

1. Abouelhoda M., Kurtz S., and Ohlebusch E. Replacing Suffix Trees with Enhanced Suffix Arrays. In Journal of Discrete Algorithms, 2:53-86, 2004.
2. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic Local Alignment Search Tool. In J. Mol. Biol., 215:403-10, 1990.
3. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., and Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. In Nucleic Acids Research, 25:3389-3402, 1997.
4. Andersson A. and Nilsson S. Efficient Implementation of Suffix Trees. In Softw. Pract. Exp., 25(2):129-141, 1995.
5. Burkhardt S., Crauser A., Ferragina P., Lenhof H. P., Rivals E., and Vingron M. q-gram Based Database Searching Using a Suffix Array. In RECOMB, pp.77-83. ACM Press, 1999
6. Crauser A. and Ferragina P. A Theoretical and Experimental Study on the Construction of Suffix Arrays in External Memory. In Algorithmica, 32(1):1-35, 2002.
7. Delcher A. L., Kasif S., Fleischmann R.D., Peterson J., White O., and Salzberg S.L. Alignment of Whole Genomes. In Nucleic Acids Research, 27:2369-2376, 1999.
8. th Workshop Algorithm. Engineering and Experiments, 2005.
9. ExPASy Server, http://us.expasy.org/
10. Ferragina P. and Grossi R. The String B-Tree: A New Data Structure for String Searching in External Memory and its Applications. In Journal of the ACM 46(2), pp. 236-280, 1999.
11. GenBank, http://www.ncbi.nlm.nih.gov/Genbank/index.html
12. Giegerich R., Kurtz S., and Stoye J. Efficient Implementation of Lazy Suffix Trees. In Softw. Pract. Exper. 33:1035-1049, 2003.
13. Gusfield D. Algorithms on Strings, Trees and Sequences: computer science and computational biology. Cambridge University Press, 1997.
14. th ACM Conference on Information and Knowledge Management (CIKM), Bremen, Germany, 2005.
15. Hunt E., Atkinson M.P., and Irving R.W. A Database Index to Large Biological Sequences. In VLDB J., 7(3):139-148, 2001.
16. Jagadish H. V., Koudas N., and Srivastava D. On Effective Multi-dimensional Indexing for Strings. In ACM SIGMOD Conference on Management of Data, pp. 403-414, 2000.
17. Kurtz S. Reducing the Space Requirement of Suffix Trees. In Software-Practice and Experience, 29(13): 49-1171, 1999.
18. Kurtz S. Vmatch: large scale sequence analysis software, http://www.vmatch.de/
19. Kurtz S., Schleiermacher C. REPuter: Fast Computation of Maximal Repeats in Complete Genomes. In Bioinformatics, pages 426-427, 1999.
20. Manber U. and Myers G. Suffix Arrays: a new method for on-line string searches. In SIAM J. Comput., 22(5):935-948, 1993.
21. McCreight E.M. A Space-economical Suffix Tree Construction Algorithm. In Journal of the ACM, 23(2):262-272, 1976.
22. M. Morgante, A. Policriti, N. Vitacolonna, and A. Zuccolo. Structured Motifs Search. In Proc. of RECOMB '04, 2004.
23. Morrison D. R. PATRICIA - Practical Algorithm to Retrieve Information Coded in Alphanumeric. In Journal of the ACM, 15(4), pp514-534, 1968.
24. Navarro G. A Guided Tour to Approximate String Matching. In ACM Computing Surveys, 33:1:31-88, 2000.
25. Navarro G. and Baeza-Yates R. A Practical q-gram Index for Text Retrieval Allowing Errors. In CLEI Electronic Journal, 1(2), 1998.
26. Navarro G., Sutinen E., Tanninen J., and Tarhio J. Indexing Text with Approximate q-grams. In CPM2000, LNCS 1848, pp. 350-365, 2000.
27. NCBI: National Center for Biotechnology Information, http://www.ncbi.nlm. nih.gov/
28. Project Gutenberg, http://www.gutenberg.org
29. Tian, Y., Tata S., Hankins R.A., and Patel J. Practical Methods for Constructing Suffix Trees. In VLDB Journal, Vol. 14, Issue 3, pp. 281-299, Sept. 2005.
30. Ukkonen E. On-line Construction of Suffix trees. In Algorithmica 14(1995), 249-260, 1995
31. th Annual Symp. on Switching and Automata Theory, 1973.
32. Witten I. H., Moffat A., and Bell T. C. Managing Gigabytes: Compressing and Indexing Documents and Images. Morgan Kaufmann, 2nd edition, 1999.