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Volume 12   Issue 1   Year 2017
References

 

  1. Oplachko E.S., Ustinin D.M., Ustinin M.N. Cloud Computing Technologies and their Application in Problems of Computational Biology. Mathematical Biology and Bioinformatics. 2013;8(2):449-466 (in Russ.). doi: 10.17537/2013.8.449
  2. Daugelaite J., O'Driscoll A., Sleator R.An Overview of Multiple Sequence Alignments and Cloud Computing in Bioinformatics. ISRN Biomathematics. 2013;2013:1-14. doi: 10.1155/2013/615630
  3. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L.BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. doi: 10.1186/1471-2105-10-421
  4. Needleman S., Wunsch C.A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970;48(3):443-453. doi: 10.1016/0022-2836(70)90057-4
  5. Pankratov A., Pyatkov M., Tetuev R., Nazipova N., Dedus F.F. Search for Extended Repeats in Genomes Based on the Spectral-Analytical Method. Mathematical Biology and Bioinformatics. 2012;7(2):476-492 (in Russ.). doi: 10.17537/2012.7.476
  6. Pyatkov M.I., Pankratov A.N. SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content. Bioinformatics. 2014;30(12):1765-1766. doi: 10.1093/bioinformatics/btu095
  7. NCBI BLAST: web site. https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed 14 April 2017).
  8. Rice P., Longden I., Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics. 2000;16(6):276-277. doi: 10.1016/S0168-9525(00)02024-2
  9. Gotoh O. An improved algorithm for matching biological sequences. J. Mol. Biol. 1982;162(3):705-708. doi: 10.1016/0022-2836(82)90398-9
  10. Press W., Teukolsky S., Vetterling W., Flannery B. Numerical Recipes: The Art of Scientific Computing. Cambridge University Press; 2007. 1256 p.
  11. Myers E., Miller W. Optimal alignments in linear space. Comput. Appl. Biosci. 1988;4(1):11-17. doi: 10.1093/bioinformatics/4.1.11
  12. Hirschberg D.S. A linear space algorithm for computing maximal common subsequences. Communications of the ACM. 1975;18(6):341-343. doi: 10.1145/360825.360861
  13. Altschul S., Gish W., Miller W., Myers E., Lipman D. Basic local alignment search tool. J. Mol. Biol. 1990;215:403-410. doi: 10.1016/S0022-2836(05)80360-2
  14. Driga A., Lu P., Schaeffer J., Szafron D., Charter K., Parsons I. FastLSA: A Fast, Linear-Space, Parallel and Sequential Algorithm for Sequence Alignment. Algorithmica. 2006(45):337-375. doi: 10.1007/s00453-006-1217-y
  15. Chakraborty A., Bandyopadhyay S. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm. Scientific Reports. 2013(3):1746. doi: 10.1038/srep01746
  16. Loving J., Hernandez Y., Benson G. BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm. Bioinformatics. 2014;30(22):3166-3173. doi: 10.1093/bioinformatics/btu507
  17. Farrar M. Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics. 2007;23(2):156-161. doi: 10.1093/bioinformatics/btl582
  18. Huson D., Chao Xie C. A poor man’s BLASTX - high-throughput metagenomic protein database search using PAUDA. Bioinformatics. 2014;30(1):38-39. doi: 10.1093/bioinformatics/btt254
  19. Galvez S., Diaz D., Hernandez P., Esteban F.J., Caballero J.A., Dorado G. Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment. Bioinformatics. 2010(26):683-686. doi: 10.1093/bioinformatics/btq017
  20. Blom J., Jakobi T., Doppmeier D., Jaenicke S., Kalinowski J., Stoye J., Goesmann A. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics. 2011(27):1351-1358. doi: 10.1093/bioinformatics/btr151
  21. Levenshtein V.I. Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics Doklady. 1966;10:707–10.
  22. Dayhoff M., Schwartz R., Orcutt B. A model of Evolutionary Change in Proteins. Atlas of protein sequence and structure. 1978;5:345-358.
  23. Henikoff S., Henikoff G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 1992;89(22):10915-10919. doi: 10.1073/pnas.89.22.10915
  24. Hamming R.W. Error Detecting and Error Correcting Codes. The Bell System Technical Journal. 1950;29(2):147-160. doi: 10.1002/j.1538-7305.1950.tb00463.x
  25. Xuhua X. In: Bioinformatics and the Cell. Modern Computational Approaches in Genomics, Proteomics and Transcriptomics. Springer, 2007:124-127.
  26. Ibarra I., Melo F. Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming. Bioinformatics. 2010;26(13):1664-1669. doi: 10.1093/bioinformatics/btq252
Table of Contents
Original Article
Ruslan K. Tetuev, Maxim I. Pyatkov, Anton N. Pankratov Parallel algorithm for global alignment of long aminoacid and nucleotide sequences. Ìàthematical biology and bioinformatics. 2017;12(1):137-150. doi: 10.17537/2017.12.137
(published in Russian)

Abstract (rus.)
Abstract (eng.)
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