A unifying framework for seed sensitivity and its application to subset seeds

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 2, 2006, Pages 553-569

  Kucherov, Gregory ^a   Noé, Laurent ^a   Roytberg, Mikhail ^b  

^a ECOLE CENTRALE DE LILLE   (France)

^b IMPB   (Russian Federation)

Author keywords

Finite automaton; Sensitivity; Sequence alignment; Similarity search; Spaced seed; Subset seed

Indexed keywords

AUTOMATION; BIOINFORMATICS; CONFERENCE PAPER; CONTROLLED STUDY; DNA SEQUENCE; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; NUCLEOTIDE SEQUENCE; PROBABILITY; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 33745726523     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006001977     Document Type: Conference Paper

References (23)

1. Aho AV, Corasick MJ, Efficient string matching: An aid to bibliographic search, Communications of the ACM 18(6):333-340, 1975.
2. Altschul S, Madden T, Schäffer A et al., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res 25(17):3389-3402, 1997.
3. Brejova B, Brown D, Vinar T, Optimal spaced seeds for Hidden Markov Models, with application to homologous coding regions, in Crochemore M, Baeza-Yates R, Chavez E (eds.) Proc 14th Symp Combinatorial Pattern Matching, Morelia (Mexico), Lecture Notes Computer Science, Vol. 2676 (Springer, 2003), pp. 42-54.
4. Brejova B, Brown D, Vinar T, Vector seeds: An extension to spaced seeds allows substantial improvements in sensitivity and specificity, in Benson G, Page R (eds.) Proc 3rd Int Workshop Algorithms Bioinformatics (WABI), Budapest (Hungary), Lecture Notes Computer Science, Vol. 2812 (Springer, 2003).
5. Brejova B, Brown D, Vinar T, Optimal spaced seeds for homologous coding regions, J Bioinformatics Computational Biol 1(4):595-610, 2004.
6. Brown D, Optimizing multiple seeds for protein homology search, IEEE Trans Computational Biol Bioinformatics 2(1):29-38, 2005.
7. Buhler J, Keich U, Sun Y, Designing seeds for similarity search in genomic DNA, in Proc 7th Annu Int Conf Computational Mol Biol (RECOMB03), ACM Press, Berlin (Germany), pp. 67-75, 2003.
8. Burkhardt S, Kärkkäinen J, Better filtering with gapped q-grams, Fundamenta Informaticae 56(1-2):51-70, 2003; preliminary version in Combinatorial Pattern Matching, 2001.
9. Chen W, Sung W, On half gapped seed, Genome Informatics 14:176-185, 2003; preliminary version in the 14th International Conference on Genome Informatics (GIW).
10. Choi KP, Zeng F, Zhang L, Good spaced seeds for homology search, Bioinformatics 20:1053-1059, 2004.
11. Choi KP, Zhang L, Sensitivity analysis and efficient method for identifying optimal spaced seeds, J Comput Sys Sci 68:22-40, 2004.
12. Finkelstein AV, Roytberg MA, Computation of biopolymers: A general approach to different problems, BioSystems 30(1-3):1-19, 1993.
13. Keich U, Li M, Ma B, Tromp J, On spaced seeds for similarity search, Discrete Applied Mathematics 138(3):253-263, 2004; preliminary version in 2002.
14. Kent JW, BLAT-the BLAST-like alignment tool, Genome Res 12(1):656-664, 2002.
15. Kucherov G, Noé L, Ponty Y, Estimating seed sensitivity on homogeneous alignments, in Proc IEEE 4th Symp Bioinformatics Bioengineering (BIBE 2004), May 19-21, 2004, Taichung (Taiwan), IEEE Computer Society Press, pp. 387-394, 2004.
16. Kucherov G, Noé L, Roytberg M, Multiseed lossless filtration, IEEE Trans Computational Biol Bioinformatics 2(1):51-61, 2005.
17. Li M, Ma B, Kisman D, Tromp J, PatternHunter II: Highly sensitive and fast homology search, J Bioinformatics Computational Biol 2004; Earlier version in GIW 2003 (International Conference on Genome Informatics).
18. Ma B, Tromp J, Li M, PatternHunter: Faster and more sensitive homology search, Bioinformatics 18(3):440-445, 2002.
19. Noé L, Kucherov G, Improved hit criteria for DNA local alignment, BMC Bioinformatics 5(149), 2004.
20. Sun Y, Buhler J, Designing multiple simultaneous seeds for DNA similarity search, in Proc 8th Annu Int Conf Computational Mol Biol (RECOMB04), San Diego (California), ACM Press, 2004.
21. Ullman J, Aho A, Hopcroft J, The Design and Analysis of Computer Algorithms, Addison-Wesley, Reading, 1974.
22. Xu J, Brown D, Li M, Ma B, Optimizing multiple spaced seeds for homology search, in Proc 15th Symp Combinatorial Pattern Matching, Istambul (Turkey), Lecture Notes Computer Science, Vol. 3109 (Springer, 2004), pp. 47-58.
23. Yang I, Wang S, Chen Y et al., Efficient methods for generating optimal single and multiple spaced seeds, in Proc IEEE 4th Symp Bioinformatics Bioengincering (BIBE 2004), May 19-21, 2004, Taichung (Taiwan), IEEE Computer Society Press, 2004, pp. 411-416.