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Hybrid Bio-Inspired Algorithms for Protein Multiple Sequence Alignment

This paper presents a novel approach to protein multiple sequence alignment (MSA) using hybrid bio-inspired algorithms. The method, termed Immunological Multiple Sequence Alignment (IMSA), incorporates cloning and hypermutation operators to enhance alignment accuracy. The study outlines the challenges of MSA, various strategies for initializing populations, and the performance of IMSA against classical benchmarks. Results show that IMSA outperforms existing methods such as CLUSTALW in certain alignment tests, providing insights into more effective sequence alignment techniques for biological applications.

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Hybrid Bio-Inspired Algorithms for Protein Multiple Sequence Alignment

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  1. Protein multiple sequence alignment by hybrid bio-inspired algorithmsVincenzo Cutello, Giuseppe Nicosia*, Mario Pavone and Igor PrizziNucleic Acids Research, 2011 • D00922025 黃任鋒 • R00922102 張庭耀 • R00922156 陳子筠 • R99922158 蘇宏麒 1

  2. Outline • Introduction & background • IMSA • Cloning and hypermutation operators • Results • Conclusion

  3. Introduction and BackgroundD00922025 黃任鋒 3

  4. About this paper 4

  5. Problem of MSA 5

  6. Methods for MSA 6

  7. Progressive alignments 7

  8. Exact algorithms 8

  9. Survey of MSA 9

  10. Outline • Introduction & background • IMSA • Cloning and hypermutation operators • Results • Conclusion

  11. Immunological Multiple Sequence Alignment(IMSA)R00922102 張庭耀 11

  12. IMSA • Two different strategies to create the initial population • New hypermutation operators • solving protein MSA that insert or remove gaps • Gap columns, which have been matched, are moved to the end of the sequence • The remaining elements(i.e. amino acids) and existing gaps are shifted into the freed space 12

  13. IMSA • Considers antigens (Ags) and B cells • Ag is a given MSA instance, i.e. the protein sequences to align • B cells are a population of alignments that have solved(or approximated) the initial problem 13

  14. 14

  15. 15

  16. Initial population strategies 16

  17. Random_initialization 17

  18. Random_initialization 18

  19. CLUSTALW-seeding 19

  20. Outline • Introduction & background • IMSA • Cloning and hypermutation operators • Results • Conclusion

  21. IMSA-Cloning and hypermutation operatorsR00922156 陳子筠 21

  22. Cloning and hypermutation operators • Represented by “Static cloning operators” • Clones B cells dup times • P(clo) of Nc = d * dup B cells, d is population size 22

  23. Cloning and hypermutation operators 23

  24. InsGap 24

  25. InsGap P(gap) 25

  26. RemGap P(gap) 26

  27. BlockShuffling operator • Select randomly start point in a sequence • BlockMove • BlockSplitHor • BlockSplitVer 27

  28. BlockMove P(block) 28

  29. BlockSplitHor P(block) 29

  30. BlockSplitVer P(block) 30

  31. STRIP_GAPS 31

  32. Aging operator • Eliminates old B cells in populations P(t), P(gap) and P(block) • The generation number of B cell is τB • New population P(t+1) of d B cells selected best survivors by (μ+λ) - selection 32

  33. 33

  34. Outline • Introduction & background • IMSA • Cloning and hypermutation operators • Results • Conclusion

  35. ResultsR99922158 蘇宏麒 35

  36. Classical Benchmark • BAliBASE version 1.0, 2.0 and 3.0 • A benchmark alignment database . • The evaluation of multiple sequence alignment. 36

  37. BAliBASE version 1.0 • 141 reference alignments • 5 reference sets 37

  38. BAliBASE version 1.0, cont. • Reference 1: equi-distant sequences with various levels of conservation • Reference 2: family aligned with a highly divergent “orphan” sequence • Reference 3: subgroups with < 25% residue identity between groups • Reference 4: sequences with N/C-terminal extensions • Reference 5: internal insertion 38

  39. BAliBASE version 2.0 • Include all alignments in version 1.0 • Alignments are verified and corrected 39

  40. BAliBASE version 3.0 • same as version 2.0 • contains 218 alignments 40

  41. IMSA - reference 1 lad2 41

  42. IMSA - reference 1 laym3 42

  43. IMSA - reference 1 1hfh 43

  44. IMSA - reference 1 2mhr 44

  45. IMSA - Reference 3 luky 45

  46. IMSA - Reference 5 1qpg 46

  47. IMSA - BAliBASE 1.0 47

  48. IMSA vs CLUSTALW-seeding - BAliBASE 1.0 48

  49. IMSA - BAliBASE 2.0 49

  50. IMSA vs CLUSTALW-seeding - BAliBASE 2.0 50

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