A randomized Numerical Aligner (rNA)

Journal of Computer and System Sciences

Volumn 78, Issue 6, 2012, Pages 1868-1882

  Policriti, Alberto ^a,b   Tomescu, Alexandru I ^a,c   Vezzi, Francesco ^a,b  

^a UNIVERSITY OF UDINE   (Italy)

^b Istituto di Genomica Applicata (IGA)   (Italy)

^c UNIVERSITY OF BUCHAREST   (Romania)

Author keywords

Approximate string matching; Hamming distance; Next Generation Sequencing; Sequencing; Short string aligner

Indexed keywords

HAMMING DISTANCE;

APPROXIMATE STRING MATCHING; AVERAGE COMPLEXITY; GENOMIC SEQUENCE; NEXT-GENERATION SEQUENCING; PATTERN LENGTH; READING ERRORS; SEQUENCING; SHORT STRING ALIGNER;

STRING SEARCHING ALGORITHMS;

EID: 84866315818     PISSN: 00220000     EISSN: 10902724     Source Type: Journal    
DOI: 10.1016/j.jcss.2011.12.007     Document Type: Conference Paper

References (33)

1. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 17 1997 3389 3402
2. W.J. Kent BLAT - The BLAST-like alignment tool Genome Res. 12 4 2002 656 664
3. D.E. Knuth, J.H. Morris, and V.R. Pratt Fast pattern matching in strings SIAM J. Comput. 6 2 1977 323 350
4. R.S. Boyer, and J.S. Moore A fast string searching algorithm Commun. ACM 20 10 1977 762 772
5. R. Karp, and M. Rabin Efficient randomized pattern-matching algorithms IBM J. Res. Develop. 31 2 1987 249 260
6. R. Li, C. Yu, Y. Li, T.-W. Lam, S.-M. Yiu, K. Kristiansen, and J. Wang SOAP2: an improved ultrafast tool for short read alignment Bioinformatics 25 15 2009 1966 1967
7. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 14 2009 1754 1760
8. B. Langmead, C. Trapnell, M. Pop, and S. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 10 3 2009 R25
9. D.S. Horner, G. Pavesi, T. Castrignano, P.D. De Meo, S. Liuni, M. Sammeth, E. Picardi, and G. Pesole Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing Briefings Bioinformatics 2009 bbp046+
10. P. Weiner, Linear pattern matching algorithms, in: Proc. 14th Ann. Symp. on Switching and Automata Theory (SWAT 1973), 1973, pp. 1-11.
11. A. Apostolico The myriad virtues of sub-word trees Combinatorics on Words 112 1985 85 96
12. E. Ukkonen, Approximate string matching over suffix trees, in: Proc. 4th Ann. Symp. on Combinatorial Pattern Matching, 1993, pp. 228-242.
13. U. Manber, G. Myers, Suffix arrays: A new method for on-line string searches, in: SODA'90: Proc. 1st Ann. ACM-SIAM Symp. on Discrete Algorithms, 1990, pp. 319-327.
14. P. Ferragina, String algorithms and data structures, CoRR abs/0801.2378.
15. K. Abrahamson Generalized string matching SIAM J. Comput. 16 6 1987 1039 1051
16. G.M. Landau, U. Vishkin, Efficient string matching in the presence of errors, in: Proc. 26th IEEE Symp. on Foundations of Computer Science, 1985, pp. 126-136.
17. G.M. Landau, and U. Vishkin Efficient string matching with k mismatches Theoret. Comput. Sci. 43 1986 239 249
18. Z. Galil, and R. Giancarlo Improved string matching with k mismatches SIGACT News 17 4 1986 52 54
19. L. Salmela, J. Tarhio, and P. Kalsi Approximate Boyer-Moore string matching for small alphabets Algorithmica 58 3 2010 591 609
20. Z. Liu, X. Chen, J. Borneman, and T. Jiang A fast algorithm for approximate string matching on gene sequences Proc. 16th Ann. Symp. on Combinatorial Pattern Matching Lecture Notes in Comput. Sci. vol. 3537 2005 79 90
21. W.I. Chang, T.G. Marr, Approximate string matching and local similarity, in: Proc. 5th Ann. Symp. on Combinatorial Pattern Matching, 1994, pp. 259-273.
22. A. Amir, M. Lewenstein, and E. Porat Faster algorithms for string matching with k mismatches J. Algorithms 50 2004 257 275
23. P. Jokinen, and E. Ukkonen Two algorithms for approximate string matching in static texts Proc. 2nd Ann. Symp. on Mathematical Foundations of Computer Science Lecture Notes in Comput. Sci. vol. 520 1991 240 248
24. T.N.D. Huynh, W.-K. Hon, T.-W. Lam, and W.-K. Sung Approximate string matching using compressed suffix arrays Theoret. Comput. Sci. 352 1 2006 240 249
25. R. Grossi, and J.S. Vitter Compressed suffix arrays and suffix trees with applications to text indexing and string matching SIAM J. Comput. 35 2 2005 378 407
26. R. Muth, U. Manber, Approximate multiple string search, in: Proc. 7th Ann. Symp. on Combinatorial Pattern Matching, 1996, pp. 75-86.
27. n ± 1) addition and multiplication IEEE Symposium on Computer Arithmetic 1999 IEEE Computer Society 158 167
28. T.H. Cormen, C.E. Leiserson, R.L. Rivest, and C. Stein Introduction to Algorithms 2nd edition 2001 MIT Press/McGraw-Hill Book Company
29. P. Ferragina, G. Manzini, Opportunistic data structures with applications, in: Proc. 41st Ann. Symp. on Foundations of Computer Science, 2000, pp. 390-398.
30. http://www.clcbio.com/files/usermanuals/CLC-Genomics-Workbench-User- Manual.pdf,
31. S. Lee, F. Hormozdiari, C. Alkan, and M. Brudno MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions Nat. Methods 6 7 2009 473 474
32. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin 1000 genome project data processing subgroup, the sequence alignment/map format and SAMtools Bioinformatics 25 16 2009 2078 2079
33. C. Del Fabbro, Repeated sequences in bioinformatics: assembly, annotation and alignments, PhD thesis, University of Udine, 2010.