Match chaining algorithms for cDNA mapping

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

Volumn 2812, Issue , 2003, Pages 462-475

  Shibuya, Tetsuo ^a   Kurochkin, Igor ^b  

^a IBM RESEARCH TOKYO   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MAPPING;

COMPUTATIONAL EXPERIMENT; INPUT MATCH; MOUSE GENOME; SUFFIX-TREES; TIME ALGORITHMS; UNIQUE MATCHES;

TREES (MATHEMATICS);

EID: 28844441737     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-39763-2_33     Document Type: Article

References (24)

1. Aho, A.V., Hopcroft, J.E. and Ullman, J.D. Data Structures and Algorithms, (1983) Addison-Wesley.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Adelson-Velskil, G.M. and Landis, E.M. (1962) Soviet Math. (Dokl.) 3, 1259-1263.
4. Bender, M.A. and Farach, M. (2000) The LCA problem revisited. Proc. Latin American Theoretical Informatics, LNCS 1776, 88-94.
5. Bentley, J. and Maurer, H. (1980) Efficient worst-case data structures for range searching. Acta Informatica, 13, 155-168.
6. Delcher, A.L., Kasif, S., Fleischmann, D., Paterson, J., White, O. and Salzberg, S.L. (1999) Alignment of whole genomes. Nucleic Acids Res., 27(11), 2369-2376.
7. Delcher, A.L., Phillippy, A., Carlton, J. and Salzberg, L. (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res., 30(11), 2478-2483.
8. FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563-573.
9. Farach, M. (1997) Optimal suffix tree construction with large alphabets. Proc. 38th IEEE Symp. Foundations of Computer Science, 137-143.
10. Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M. and Miller, W. (1998) A computer program for aligning a cDNA Sequence with a Genomic DNA Sequence. Genome Res., 8, 967-974.
11. Gelfand, M.S., Mironov, A.A. and Pevzner, P.A. (1996) Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. USA, 93, 9061-9066.
12. Gusfield, D. (1997) Algorithms on strings, trees, and sequences: computer science and computational biology, Cambridge University Press.
13. Hoehl, M., Kurtz, S. and Ohlebusch, E. (2002) Efficient multiple genome alignment. Bioinformatics, 18(Suppl. 1), 8312-320.
14. Kent, W. J. (2002) The BLAST-like alignment tool. Genome Res., 12, 656-664.
15. Labrador, M., Mongelard, F., Plata-Rengifo, P., Bacter, E.M., Corces, V.G. and Gerasimova, T.I. (2001) Protein encoding by both DNA strands. Nature, 409, 1000.
16. Manber, U. and Myers, G. (1993) Suffix arrays: a new method for on-line string searches. SIAM J. Comput., 22(5), 935-948.
17. McCreight, E.M. (1976) A space-economical suffix tree construction algorithm. J. ACM, 23, 262-272.
18. Mott, R. (1997) EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput. Applic. Biosci., 13(4), 477-478.
19. Myers, E and Miller, W. (1995) Chaining multiple-alignment fragments in subquadratic time. Proc. ACM-SIAM Symp. on Discrete Algorithms, 38-47.
20. Ogasawara, J. and Morishita, S. (2002) Fast and sensitive algorithm for aligning ESTs to Human Genome. Proc. 1st IEEE Computer Society Bioinformatics Conference, Palo Alto, CA, 43-53.
21. Sze, S-H. and Pevzner, P.A. (1997) Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. J. Comp. Biol., 4(3), 297-309.
22. Ukkonen, E. (1995) On-line construction of suffix-trees. Algorithmica, 14, 249-260.
23. Usuka, J., Zhu, W. and Brendel, V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics, 16(3), 203-211.
24. Weiner, P. (1973) Linear pattern matching algorithms. Proc. 14th Symposium on Switching and Automata Theory, 1-11.