References
- C. Gibas and P. Jambeck, Developing Bioinformatics Computer Skills, O'Reilly and Associates Inc., 2001
- Z. Tan, X. Cao, B. Ooi, and A. Tung, 'The ed-tree: An Index for Large DNA Sequence Databases,' In Proceedings of SSDBM Conference, pp. 1-10, 2003
- H. E. Williams and J. Zobel, 'Indexing and Retrieval for Genomic Databases,' IEEE TKDE Vol. 14, No. 1. pp. 63-78, 2002 https://doi.org/10.1109/69.979973
- T. Smith and M. Waterman, 'Identification of Common Molecular Subsequences,' Journal of Molecular Biology, 147, pp. 195-197, 1981 https://doi.org/10.1016/0022-2836(81)90087-5
- S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, 'Basic local alignment search tool,' Journal of Molecular Biology, Vol. 215, No.3, pp. 403-410, 1990 https://doi.org/10.1006/jmbi.1990.9999
- S. Altschul, T. Madden, A. Schaffer, J. Zhang, W. Miller, and D. Lipman, 'Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,' Nucleic Acids Research, Vol 25, No. 17, pp. 3389-3402,1997 https://doi.org/10.1093/nar/25.17.3389
- G. A. Stephen, String Searching Algorithms, World Scientific Publishing, 1994
- A. L. Deicher, S. Kasif, R. D. Fleischmann, and J. Peterson, O. White, and S. L. Salzberg, 'Alignment of whole genomes,' Nucleic Acids Research, 27, pp. 2369-2376, 1999 https://doi.org/10.1093/nar/27.11.2369
- E. Hunt, M. P. Atkinson and R. W. Irving, 'Database indexing for large DNA and protein sequence collections,' The VLDB Journal, Vol. 11, No.3, pp. 256-271, 2002 https://doi.org/10.1007/s007780200064
- S. Kurtz, J. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich, 'REPuter: the manifold applications of repeat analysis on a genome scale,' Nucleic Acids Research, Vol. 29, No. 22, pp. 4633-4642, 2001 https://doi.org/10.1093/nar/29.22.4633
- C. Meek, J. M. Patel, and S. Kasetty, 'OASIS: An Online and Accurate Technique for Local-Alignment Searches on Biological sequences,' In Proceedings of the 29th VLDB Conference, pp. 920-921, 2003
- K. Sadakane and T. Shibuya. 'Indexing huge genome sequences for solving various problems,' In Proceedings of the 12th Genome Informatics, pp. 175-183, 2001
- E. Ukkonen, 'Approximate string matching over suffix trees,' In Proceedings of Combinatorial Pattern Matching (CPM93), pp. 228-242, 1993 https://doi.org/10.1007/BFb0029808
- R. Giegerich, S. Kurtz, and J. Stoye, 'Efficient Implementation of Lazy Suffix Trees,' Softw. Pract. Exp., Vol 33, pp. 1035-1049, 2003 https://doi.org/10.1002/spe.535
- S. Kurtz, 'Reducing the Space Requirement of Suffix Trees,' Softw. Pract. Exp., Vol 29, pp. 1149-1171, 1999 https://doi.org/10.1002/(SICI)1097-024X(199911)29:13<1149::AID-SPE274>3.0.CO;2-O
- G. Navarro and R. Baeza-Yates, 'A Hybrid Indexing Method for Approximate String Matching,' J. of Discrete ALgorithms, Vol. 1, No.1, pp. 205-239, 2000
- H. Wang et al., 'BLAST++: A Tool for BLASTing Queries in Batches,' In Proceedings First Asia-Pacific Bioinformatics Conference, pp. 71-79, 2003
- E. Horowitz, S. Sahni, and S. Anderson-Freed, Fundamentals of Data Structures in C, Computer Science Press, 1993
- A. Califano and I. Rigoutso, 'FLASH: A Fast Look-up Algorithm for String Homology,' In Proceedings of Intelligent System Conference for Morecular Biology, pp. 56-64, 1993
- C. Fondrat and P. Dessen, 'A Rapid Access Motif database(RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or proteun databanks,' Computer Applications in the Biosciences. Vol. 11, No.3, pp. 273-279, 1995 https://doi.org/10.1093/bioinformatics/11.3.273
- T. Kahveci and A. K. Singh, 'An Efficient Index Structure for String Databases,' In Proceedings of the 27th VLDB Conference, pp. 351-360, 2001
- S. Tata, R. Hankins, and J. Patel, 'Practical Suffix Tree Construction,' In Proceedings of the 30th VLDB Conference, pp. 36-47, 2004
- K. Kelly and P. Labute, 'The A* Search and Applications to Sequence Alignment,' http://www.chemcomp.com/article/astar.htm, 1996
- U. Manber and G. Myers, 'Suffix arrays: A new method for on-line string searches,' SIAM J. Comput. 22, pp. 935-948, 1993 https://doi.org/10.1137/0222058
- V. Makinen, 'Compact Suffix Array: A Space efficient Full-text Index,' Fundamenta Informaticae, 56(1-2), pp. 191-210, 2003
- V. Makinen and G. Navarro, 'Compressed Compact Suffix Arrays,' CPM 2004, Springer-Verlag LNCS 3109, pp. 420-433
- H. Shang and T. H. Merrett, 'Tries for approximate string matching,' IEEE Trans. on Knowlege and Data Engineering, Vol. 8, No.4, pp. 540-547, 1996 https://doi.org/10.1109/69.536247
- http://www.ncbi.nlm.nih.gov