Multiple Sequence Alignment - Lecture 01

MULTIPLE SEQUENCEALIGNMENT

Bionformatics of Cyanobacteria and PlantsApril 2007

University of Turku

Multiple Sequence Alignment

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How Multiple Sequence AlignmentIs Used

• Prediction of structural similarities inunknown proteins based on knownproteins in the alignment

• Searches for sequences for an unknowngenome, e.g., for the design of aspecific DNA probe

• Automated assembly of large sequencesin genome sequencing or mRNAsequences from ESTs


University of Turku


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Phylogenetic Analyses May Start WithMultiple Sequence Alignments

seqA N • F L SseqB N • F – SseqC N K Y L SseqD N • Y L S

+K -L

Y to F

N Y L S N K Y L S N F S N F L S


University of Turku


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Multiple Sequence AlignmentsCan Be Global or Local

• In global msa, pair-wise aligmentis extended to include more(closely) related sequences

• Conserved domains in DNA orprotein sequences are found usinglocal msa methods


University of Turku


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Global MSA Is Done UsingApproximate Methods

• Progressive global alignment starts withaligning most-alike sequences

• Iterative methods globally align groupsof sequences and revise the result

• Alignments based on locally conservedpatterns found in the same order

• Statistical methods generatingprobalistic models

• Graph-based methods


University of Turku


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The Dynamic ProgrammingAlgorithm Limits the MSA

• Number of comparisons is the productof the lengths of sequences– Three protein sequences of each 300 amino

acids means 3003 comparisons

• Supercomputers may handle tensequences of each up to 1000 aminoacids

• Sum-of-pairs method is used– Sums the scores of all pair-wise alignments


University of Turku


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CLUSTALW Uses a ProgressiveMethod for Global MSA

• Pair-wise alignments of all sequencepairs using, e.g., FASTA

• Alignments scores are used to producea phylogenetic tree (calculated usingthe neighbor-joining method [Saitouand Nei, 1987])

• Sequences are sequentially alignedusing dynamic programming in theorder of their relationship on the tree


University of Turku


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Alignment Scores Are Weighted

• Scores for aligning similar sequencesare given a small weight, so they havea smaller effect on the msa

• Scores for aligning less similarsequences are given a larger weight

• Weighting more accurately reflectssequence changes in the phylogenetictree


University of Turku


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Gaps are placed betweenconserved domains

• When aligning structural relatedproteins gaps were found preferentiallybetween secondary structural elements(Pascarella and Argos, 1992)

• A table was prepared giving theobserved frequency of gaps next toeach amino acid in these regions

• CLUSTALW tries to locate thecorresponding domains by appropriategap placement


University of Turku


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CLUSTALW at EBI


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MSAs Can Be Viewed and EditedUsing Jalview


University of Turku


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The MUSCLE Algorithm Provides aFaster and Refined Alignment

Multiple Sequence Alignment - Lecture 01

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