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

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Outline

•Introduction & background

•IMSA

•Cloning and hypermutation operators

•Results

•Conclusion

Introduction and BackgroundD00922025 黃任鋒

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About this paper

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Problem of MSA

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Methods for MSA

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Progressive alignments

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Exact algorithms

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Survey of MSA

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Outline

•Introduction & background

•IMSA

•Cloning and hypermutation operators

•Results

•Conclusion

Immunological Multiple Sequence Alignment(IMSA)

R00922102 張庭耀

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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

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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

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Initial population strategies

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Random_initialization

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Random_initialization

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CLUSTALW-seeding

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Outline

•Introduction & background

•IMSA

•Cloning and hypermutation operators

•Results

•Conclusion

IMSA-Cloning and hypermutation operatorsR00922156 陳子筠

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Cloning and hypermutation operators

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•Represented by “Static cloning operators”

•Clones B cells dup times

•P(clo) of Nc = d * dup B cells, d is population size

Cloning and hypermutation operators

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InsGap

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InsGap P(gap)

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RemGap P(gap)

BlockShuffling operator

•Select randomly start point in a sequence

•BlockMove

•BlockSplitHor

•BlockSplitVer

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BlockMove P(block)

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BlockSplitHor P(block)

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BlockSplitVer P(block)

STRIP_GAPS

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Aging operator

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•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

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Outline

•Introduction & background

•IMSA

•Cloning and hypermutation operators

•Results

•Conclusion

ResultsR99922158 蘇宏麒

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Classical Benchmark

•BAliBASE version 1.0, 2.0 and 3.0

- A benchmark alignment database .

- The evaluation of multiple sequence alignment.

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BAliBASE version 1.0

•141 reference alignments

•5 reference sets

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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

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BAliBASE version 2.0

•Include all alignments in version 1.0

•Alignments are verified and corrected

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BAliBASE version 3.0

•same as version 2.0

•contains 218 alignments

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IMSA - reference 1 lad2

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IMSA - reference 1 laym3

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IMSA - reference 1 1hfh

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IMSA - reference 1 2mhr

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IMSA - Reference 3 luky

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IMSA - Reference 5 1qpg

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IMSA - BAliBASE 1.0

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IMSA vs CLUSTALW-seeding - BAliBASE 1.0

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IMSA - BAliBASE 2.0

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IMSA vs CLUSTALW-seeding - BAliBASE 2.0

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IMSA vs AIS - BAliBASE 2.0

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IMSA vs ClonAlign - BAliBASE 2.0

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IMSA vs COBALT, PROBCONS, PCMA, MUSCLE, CLUSTALW - BAliBASE 3.0

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IMSA - BAliBASE 3.0 - SP

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IMSA - BAliBASE 3.0 - CS

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Running time - BAliBASE 3.0

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Outline

•Introduction & background

•IMSA

•Cloning and hypermutation operators

•Results

•Conclusion

Final Remarks

•Clonal Selection Algorithm

•IMSA

•IMSA

•CLUSTALW-seeding

•Two specific ad-hoc mutation operators

•Generating more than a single suboptimal alignment, for every MSA instance.

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Final Remarks, cont.

•BAliBASE 1.0

•IMSA is superior to PRRP, CLUSTALX, SAGA, DIALIGN, PIMA, MULTIALIGN and PILEUP 8.

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Final Remarks, cont.

•BAliBASE 2.0

•high SP, low CS

•future work - improvement of the CS score

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Final Remarks, cont.

•BAliBASE 2.0

•IMSA shows best performance, and hence best alignments, than both ClonAlign and AIS.

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Final Remarks, cont.

•BAliBASE 3.0 - new testbed

•compare with state-of-the-art alignment algorithms, IMSA also shows good alignments.

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Reference

•http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE2/

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Thank you .D00922025 黃任鋒R00922102 張庭耀R00922156 陳子筠R99922158 蘇宏麒

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