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Protein multiple sequence alignment by hybrid bio-inspired algorithms Vincenzo Cutello, Giuseppe Nicosia*, Mario Pavone and Igor Prizzi Nucleic Acids Research,

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Introduction and Background D 黃任鋒 3

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Protein multiple sequence alignment by hybrid bio-inspired algorithms Vincenzo Cutello, Giuseppe Nicosia*, Mario Pavone and Igor Prizzi Nucleic Acids Research, 2011 D R R R 1 Outline Introduction & background IMSA Cloning and hypermutation operators Results Conclusion Introduction and Background D 3 About this paper 4 Problem of MSA 5 Methods for MSA 6 Progressive alignments 7 Exact algorithms 8 Survey of MSA 9 Outline Introduction & background IMSA Cloning and hypermutation operators Results Conclusion Immunological Multiple Sequence Alignment(IMSA) R 11 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 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 15 Initial population strategies 16 Random_initialization 17 Random_initialization 18 CLUSTALW-seeding 19 Outline Introduction & background IMSA Cloning and hypermutation operators Results Conclusion IMSA-Cloning and hypermutation operators R 21 Cloning and hypermutation operators 22 Represented by Static cloning operators Clones B cells dup times P (clo) of N c = d * dup B cells, d is population size Cloning and hypermutation operators 23 InsGap 24 25 InsGap P (gap) 26 RemGap P (gap) BlockShuffling operator Select randomly start point in a sequence BlockMove BlockSplitHor BlockSplitVer 27 28 BlockMove P (block) 29 BlockSplitHor P (block) 30 BlockSplitVer P (block) STRIP_GAPS 31 Aging operator 32 Eliminates old B cells in populations P (t), P (gap) and P (block) The generation number of B cell is B New population P (t+1) of d B cells selected best survivors by (+) - selection 33 Outline Introduction & background IMSA Cloning and hypermutation operators Results Conclusion Results R 35 Classical Benchmark BAliBASE version 1.0, 2.0 and A benchmark alignment database. - The evaluation of multiple sequence alignment. 36 BAliBASE version reference alignments 5 reference sets 37 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 BAliBASE version 2.0 Include all alignments in version 1.0 Alignments are verified and corrected 39 BAliBASE version 3.0 same as version 2.0 contains 218 alignments 40 IMSA - reference 1 lad2 41 IMSA - reference 1 laym3 42 IMSA - reference 1 1hfh 43 IMSA - reference 1 2mhr 44 IMSA - Reference 3 luky 45 IMSA - Reference 5 1qpg 46 IMSA - BAliBASE IMSA vs CLUSTALW-seeding - BAliBASE IMSA - BAliBASE IMSA vs CLUSTALW-seeding - BAliBASE IMSA vs AIS - BAliBASE IMSA vs ClonAlign - BAliBASE IMSA vs COBALT, PROBCONS, PCMA, MUSCLE, CLUSTALW - BAliBASE IMSA - BAliBASE SP 54 IMSA - BAliBASE CS 55 Running time - BAliBASE Outline Introduction & background IMSA Cloning and hypermutation operators Results Conclusion Final Remarks Clonal Selection Algorithm IMSA CLUSTALW-seeding Two specific ad-hoc mutation operators Generating more than a single suboptimal alignment, for every MSA instance. 58 Final Remarks, cont. BAliBASE 1.0 IMSA is superior to PRRP, CLUSTALX, SAGA, DIALIGN, PIMA, MULTIALIGN and PILEUP 8. 59 Final Remarks, cont. BAliBASE 2.0 high SP, low CS future work - improvement of the CS score 60 Final Remarks, cont. BAliBASE 2.0 IMSA shows best performance, and hence best alignments, than both ClonAlign and AIS. 61 Final Remarks, cont. BAliBASE new testbed compare with state-of-the-art alignment algorithms, IMSA also shows good alignments. 62 Referencestrasbg.fr/fr/Products/Databases/BAliBA SE2/strasbg.fr/fr/Products/Databases/BAliBA SE2/ 63 Thank you. D R R R 64