Multiple Sequence Alignment & Phylogenetic Tree

8/6/2019 Multiple Sequence Alignment & Phylogenetic Tree

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Multiple Sequence Alignment

&Phylogenetic Tree


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Multiple Sequence Alignment

Multiple sequence alignment is the process toaligning three or more sequences with each

other so as to bring as many similar sequencecharacters as possible.


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Why perform an MSA? V isualize trends between homologous sequences:

Shared regions of homology R egions unique to a sequence within a family

Structural/functional motif As the first step in a phylogenetic analysis I mprove accuracy of structure predictions


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P rogressive Multiple Alignment

H euristicPerform pairwise alignments

Align sequences to alignments or alignments toexisting alignments (profile alignments)


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I terative met hods

Several progressive alignment met hods can be iteratede.g. ClustalX


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ClustalX Algorit hm

P erform alignments and calculate distances for all pairs of sequences Construct guide tree (dendrogram) joining t he mostsimilar sequences using Neig h bour Joining Align sequences, starting at t he leaves of t he guidetree. T his involves t he pair-wise comparisons as wellas comparison of single sequence wit h a group of seqs(P rofile)


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U sing ClustalX

Start wit h sequences in FASTA format (or an existingalignment in Clustal format[Do Alignment] on t he alignment menu


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Consensus Sequences

Simplest Form:A single sequence w hich represents t he most common amino acid/basein that position

Y D D G A V - E A LY D G G - - - E A LF E G G I L V E A LF D - G I L V Q A VY E G G A V V Q A LY D G G A/I V/L V E A L


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ClustalX P arameters

Scoring Matrix Gap opening penalt y Gap extension penalt y

P rotein gap parameters Additional algorit hm parameters Secondar y structure penalties


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Score Matrices

P airwise matrices and multiple alignmentmatrix series

PAM (Da yhoff), BLOS U M (Hennikof),GONNET (default), user definedTransition (AG)/Transversion (C


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Gap P enalties

Linear gap penalties Affine gap penaltiesp = (o + l.e)

Gap openingGap extension

P rotein specific penalties (on b y default)-I ncrease t he probabilit y of gaps associated

with certain residues-I ncrease t he chances of gaps in loop

regions (> 5 hydrop hilic residues)


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Algorit hm parameters

Slow-accurate pair-wise alignment Do alignment from guide tree Reset gaps before aligning (iteration) Dela y Divergent sequences (%)


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Additional displa ys

Column ScoresLow qualit y regionsExceptional residues


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Multiple Alignment Strategies

Align pairs of sequences using an optimal met hodC hoose representative sequences to align carefull yC hoose sequences of comparable lengt hsP rogressive alignment programs suc h as ClustalX for multiple alignment

P rogressive alignment programs ma y be combined

Review alignment b y eye and edit


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1 MITTENS1 MITTENS2 KITTIES2 KITTIES3 SMITTEN3 SMITTEN4 KITTE4 KITTE

11

33

44

22

11 --MITTENSMITTENS3 SMITTEN3 SMITTEN--

13 MITTEN13 MITTEN

13 MITTEN13 MITTEN4 KITTENS4 KITTENS

134 ITTEN134 ITTEN

Manual editing:Fine adjustment of particular columns

Incorporate specific knowledgeRemoval of gappy bits

Important for phylogenetic analysisRemoval of parts of/whole sequences

Non-homologous regionsSequences included by error


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Multiple Alignments & P hylogenetic

TreesYou can make a more accurate multiplesequence alignment if you know t he tree

alread yA good multiple sequence alignment is animportant starting point for drawing a treeT he process of constructing a multiplealignment (unlike pair-wise) needs to takeaccount of p hy logenetic relations hips


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P hylogenetic Tree

A p hy logenetic tree is a representation of t heevolutionar y/geneological relations hips between acollection of organisms (or molecular sequences).


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Components of Tree

Node St yleTerminal Nodes

I nternal NodesRootBranc hesFont St yle


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Met hods For Tree Building

C ladistic Approach-Maximum Parsimony Method

-Maximum Likelihood MethodPhenetic Approach

-Neighbour Joining (NJ method)


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Editing a multiple sequence alignment

I t is NOT fraud to edit a multiple sequence alignmentI ncorporate additional knowledge if possible

Alignment editors help to keep t he data organized andhelp to prevent unwanted mistakes.e.g. Bioedit, Seaview, Jalview etc.


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P rofile Alignment

P osition specific scoresAllows alignment of alignmentsGaps introduced as w hole columns in t he separatealignmentsOptimal alignment in time O(a2l2)

I nformation about t he degree of conservation of

sequence positions is included


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Thank You

Documents

Multiple Sequence Alignment & Phylogenetic Tree