References

  1. Karel Břinda (2013): Laser method on-line. Available at http://brinda.cz/laser-method/.
  2. Karel Břinda (2013): Lossless seeds for approximate string matching. FNSPE Czech Technical University in Prague, Czech Republic. Available at http://brinda.cz/publications/diplomka.pdf.
  3. Stefan Burkhardt & Juha Kärkkäinen (2001): Better Filtering with Gapped q-Grams. In: Proceedings of the 12th Symposium on Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science 2089. Springer, pp. 73–85, doi:10.1007/3-540-48194-X_6.
  4. Stefan Burkhardt & Juha Kärkkäinen (2002): Better filtering with gapped q-grams. Fundamenta Informaticae 56(1-2), pp. 51–70.
  5. Yangho Chen, Tate Souaiaia & Ting Chen (2009): PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25(19), pp. 2514–2521, doi:10.1093/bioinformatics/btp486.
  6. Lavinia Egidi & Giovanni Manzini (2011): Spaced Seeds Design Using Perfect Rulers. In: Proceedings of the 18th International Symposium on String Processing and Information Retrieval (SPIRE), Pisa (Italy), Lecture Notes in Computer Science 7024. Springer, pp. 32–43, doi:10.1007/978-3-642-24583-1_5.
  7. Lavinia Egidi & Giovanni Manzini (2013): Better spaced seeds using quadratic residues. Journal of Computer and System Sciences 79(7), pp. 1144–1155, doi:10.1016/j.jcss.2013.03.002.
  8. Lavinia Egidi & Giovanni Manzini (2014): Design and analysis of periodic multiple seeds. Theoretical Computer Science 522, pp. 62–76, doi:10.1016/j.tcs.2013.12.007.
  9. Lavinia Egidi & Giovanni Manzini (2014): Spaced Seeds Design Using Perfect Rulers. Fundamenta Informaticae 131(2), pp. 187–203, doi:10.3233/FI-2014-1009.
  10. Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp & Dekel Tsur (2007): Optimal spaced seeds for faster approximate string matching. Journal of Computer and System Sciences 73(7), pp. 1035–1044, doi:10.1016/j.jcss.2007.03.007.
  11. Gregory Kucherov, Laurent Noé & Mikhail A. Roytberg (2005): Multiseed lossless filtration. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 2(1), pp. 51–61, doi:10.1109/tcbb.2005.12.
  12. Heng Li & Nils Homer (2010): A survey of sequence alignment algorithms for next-generation sequencing.. Briefings in bioinformatics 11(5), pp. 473–83, doi:10.1093/bib/bbq015.
  13. Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma & Ming Li (2008): ZOOM! Zillions Of Oligos Mapped. Bioinformatics 24(21), pp. 2431–2437, doi:10.1093/bioinformatics/btn416.
  14. Douglas Lind & Brian Marcus (1995): An Introduction to Symbolic Dynamics and Coding. Cambridge University Press, doi:10.1017/CBO9780511626302.
  15. M. Lothaire (1983): Combinatorics on Words. Encyclopedia of Mathematics and its Applications 17. Addison-Wesley Publishing Co., Reading, Mass., doi:10.1017/CBO9780511566097. Reprinted in the Cambridge University Press, Cambridge, UK, 1997.
  16. Bin Ma, John Tromp & Ming Li (2002): PatternHunter: Faster and more sensitive homology search. Bioinformatics 18(3), pp. 440–445, doi:10.1093/bioinformatics/18.3.440.
  17. Saul B Needleman & Christian D Wunsch (1970): A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48(3), pp. 443–453, doi:10.1016/0022-2836(70)90057-4.
  18. François Nicolas & Éric Rivals (2005): Hardness of Optimal Spaced Seed Design. In: A. Apostolico, M. Crochemore & K. Park: Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM), Jeju Island (Korea), Lecture Notes in Computer Science 3537. Springer, pp. 144–155, doi:10.1007/b137128.
  19. François Nicolas & Éric Rivals (2008): Hardness of Optimal Spaced Seed Design. Journal of Computer and System Sciences 74(5), pp. 831–849, doi:10.1016/j.jcss.2007.10.001.
  20. Laurent Noé (2014): Spaced seeds bibliography. Available at http://www.lifl.fr/~noe/spaced_seeds.html.
  21. Laurent Noé & Gregory Kucherov (2005): YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Research 33(suppl. 2), pp. W540–W543, doi:10.1093/nar/gki478.
  22. Paolo Ribeca (2012): Short-Read Mapping. In: Naiara Rodríguez-Ezpeleta, Michael Hackenberg & Ana M. Aransay: Bioinformatics for High Throughput Sequencing. Springer New York, pp. 107–125, doi:10.1007/978-1-4614-0782-9_7.
  23. Temple F. Smith & Michael S. Waterman (1981): Identification of common molecular subsequences.. Journal of molecular biology 147(1), pp. 195–7, doi:10.1016/0022-2836(81)90087-5.
Comments and questions to: eptcs@eptcs.org
For website issues: webmaster@eptcs.org