|
[Alt86] S. Altschul and B.W. Erickson, Optimal sequence alignment using affine gap costs. Journal of Molecular Biology, 48(5-6):603-616, 1986. [Alt90] S. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipma, Basic Local Alignment Search Tool. Journal of Molecular Biology, 215(3):403-410, 1990. [Alt96] S. Altschul and W. Gish, Local Alignment Statistics. Methods Enzymol, 266:460-480, 1996. [Alt97] S. Altschul, T.L. Madden, A.A. Schaffer, 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 Research, 25(17):3389-3402, 1997. [Bae92] R.A. Baeza-Yates and C.H. Perleberg, Fast and practical approximate string matching. In Combinatorial Pattern Matching, 185-192, 1992. [Bae97] R.A. Baeza-Yates and G. Navarro, A practical index for text retrieval allowing errors. In Conferencia Latinoamericana de Informática volume1, 273-282, 1997. [Bae99] R.A. Baeza-Yates and G. Nabarro, Faster Approximate string matching. Algorithmica, 23(2):127-158, 1999. [Ben00] D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, B.A. Rapp, and D.L. Wheeler, Genbank. Nucleic Acids Research, 26(1):1–7, 2000. [Dec02] A. Delcher, A. Phillippy, J. Carlton, and S.L. Salzberg, Fast Algorithms for Large-scale Genome Alignment and Comparison. Nucleic Acids Research, 30(11):2478-2483, 2002. [Del99] A. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg, Alignment of Whole Genomes. Nucleic Acids Research, 27(11):2369-2376, 1999. [Dur98] R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence analysis. Cambridge University press, 1 edition, 12-34 1998. [Fer01] P. Ferragina and G. Manzini, An Experimental Study of an Opportunistic Index. In Proc. of ACM-SIAM Symposium on Discrete Algorithms, 269-278, 2001. [Gus97] D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University press, 1 edition, 1997. [Hun03] E. Hunt, The Suffix Sequoia Index for Approximate String Matching. Department of Computing Science, University of Glasgow, Glasgow, UK, TR 2003-135, 2003. [Kah01] T. Kahveci and A.K. Singh, An Efficient Index Structure for String Databases. Very Large Data Bases, 351-360, 2001. [Kur01] S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich, REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale. Nucleic Acids Research, 29(22):4633-4642, 2001. [Man93] U. Manber and E. Myers, Suffix Arrays: A New Method for On-line String Searches. SIAM Journal on Computing, 22(5):935-948, 1993. [Mee03] C. Meek, J.M. Patel, and S. Kasetty, OASIS: An Online and Accurate Technique for Local-alignment Searches on Biological Sequences. Very Large Data Bases, 910–921, 2003. [Mye86] E. Myers, An O(ND) difference algorithm and its variations. Algorithmica, 251-266, 1986. [Mye94] E. Myers, A sublinear algorithm for approximate keyword matching. Algorithmica, 345-374, 1994. [Nas01] H. Nash and D. Blair, Comparing Algorithm for Largescale Sequence Analysis. Bioinformatic and Bioengineering, 89-96, 2001. [Pea88] W.R. Pearson and D.J. Lipman, Improved Tools for Biological Sequence Comparison. Proceedings of the National academy of Sciences,85(8):2444-2448, 1988. [Sah03] S.C. Sahinalp, M. Tasan, J. Macker, Z.M. Ozsoyoglu, , Distance Based Indexing for String Proximity Search. International Conference on Data Engineering, 125-136, 2003. [She05] S.Sheu, A. Chang, and W. Hang, Fast Similarity Search in String Database. Advanced Information Networking and Applications, 617-622, 2005. [Shp96] E.G. Shpaer, M. Robinson, D. Yee, J.D. Candlin, R. Mines, T. Hunkapiller., Sensitivity and Selectivity in Protein Similarity Searches: A Comparison of Smith-Waterman in Hardware to BLAST and FASTA. Genomics, 38:179-191, 1996. [Smi81] T. Smith and M. Waterman, Identification of Common Molecular Subsequences. Journal of Molecular Biology, 147:195-197, 1981. [Tat04] S. Tata, R.A. Hankins, and J.M. Patel, Practical Suffix Tree Construction. Very Large Data Bases, 36-47, 2004. [Uli99] S. Uliel, A. Fliess, A. Amir, and R. Unger, A simple algorithm for detecting circular permutations in proteins. Bioinformatics, 15(11):930-936, 1999. [Wu92] S. Wu, and U. Manber, Fast text searching allowing errors. Communications of the ACM, 35(10):83-91, 1992.
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