Contents

Index

multialign - Align multiple sequences using progressive method

Syntax

SeqsMultiAligned = multialign(Seqs) SeqsMultiAligned = multialign(Seqs, Tree) multialign(..., 'PropertyName', PropertyValue,...) multialign(..., 'Weights', WeightsValue) multialign(..., 'ScoringMatrix', ScoringMatrixValue) multialign(..., 'SMInterp', SMInterpValue) multialign(..., 'GapOpen', GapOpenValue) multialign(..., 'ExtendGap', ExtendGapValue) multialign(..., 'DelayCutoff', DelayCutoffValue) multialign(..., 'UseParallel', UseParallelValue) multialign(..., 'Verbose', VerboseValue) multialign(..., 'ExistingGapAdjust', ExistingGapAdjustValue) multialign(..., 'TerminalGapAdjust', TerminalGapAdjustValue)

Arguments

`Seqs`	Vector of structures with the fields `'Sequence'` for the residues and `'Header'` or `'Name'` for the labels. `Seqs` can also be a cell array of strings or a char array.
`Tree`	Phylogenetic tree calculated with the `seqlinkage` or `seqneighjoin` function.
`WeightsValue`	Property to select the sequence weighting method. Enter `'THG'` (default) or `'equal'`.
`ScoringMatrixValue`	Property to select or specify the scoring matrix. Enter an `[MxM]` matrix or `[MxMxN]` array of matrixes with `N` user-defined scoring matrices. `ScoringMatrixValue` can also be a cell array of strings with matrix names. The default is the `BLOSUM80` to `BLOSUM30` series for amino acids or a fixed matrix NUC44 for nucleotides. When passing your own series of scoring matrices, ensure they share the same scale.
`SMInterpValue`	Property to specify whether linear interpolation of the scoring matrices is on or off. When `false`, the scoring matrix is assigned to a fixed range depending on the distances between the two profiles (or sequences) being aligned. Default is `true`.
`GapOpenValue`	Scalar or a function specified using `@`. If you enter a function, `multialign` passes four values to the function: the average score for two matched residues (`sm`), the average score for two mismatched residues (`sx`), and, the length of both profiles or sequences (`len1`, `len2`). Default is `@(sm,sx,len1,len2) 5*sm`.
`ExtendGapValue`	Scalar or a function specified using `@`. If you enter a function, `multiialign` passes four values to the function: the average score for two matched residues (`sm`), the average score for two mismatched residues (`sx`), and the length of both profiles or sequences (`len1`, `len2`). Default is `@(sm,sx,len1,len2) sm/4`.
`DelayCutoffValue`	Property to specify the threshold delay of divergent sequences. Default is unity where sequences with the closest sequence farther than the median distance are delayed.
`UseParallelValue`	Controls the computation of the pairwise alignments using `parfor`-loops. When `true`, and Parallel Computing Toolbox™ is installed and a MATLAB pool is open, computation occurs in parallel. If Parallel Computing Toolbox is not installed, or a MATLAB pool is not open, then computation uses `parfor`-loops in serial mode. Default is `false`, which uses `for`-loops in serial mode.
`VerboseValue`	Property to control displaying the sequences with sequence information. Default is `false`.
`ExistingGapAdjustValue`	Property to control automatic adjustment based on existing gaps. Default is `true`.
`TerminalGapAdjustValue`	Property to adjust the penalty for opening a gap at the ends of the sequence. Default is `false`.

Return Values

SeqsMultiAligned

Vector of structures (same as Seqs) but with the field 'Sequence' updated with the alignment.

When Seqs is a cell or char array, SeqsMultiAligned is a char array with the output alignment following the same order as the input.

Description

SeqsMultiAligned = multialign(Seqs) performs a progressive multiple alignment for a set of sequences (Seqs). Pairwise distances between sequences are computed after pairwise alignment with the Gonnet scoring matrix and then by counting the proportion of sites at which each pair of sequences are different (ignoring gaps). The guide tree is calculated by the neighbor-joining method assuming equal variance and independence of evolutionary distance estimates.

SeqsMultiAligned = multialign(Seqs, Tree) uses a tree (Tree) as a guide for the progressive alignment. The sequences (Seqs) should have the same order as the leaves in the tree (Tree) or use a field ('Header' or 'Name') to identify the sequences.

multialign(..., 'PropertyName', PropertyValue,...) enters optional arguments as property name/property value pairs. Specify one or more properties in any order. Enclose each PropertyName in single quotation marks. Each PropertyName is case insensitive. These property name/property value pairs are as follows:

multialign(..., 'Weights', WeightsValue) selects the sequence weighting method. Weights emphasize highly divergent sequences by scaling the scoring matrix and gap penalties. Closer sequences receive smaller weights.

Values of the property Weights are:

'THG' (default) — Thompson-Higgins-Gibson method using the phylogenetic tree branch distances weighted by their thickness.
'equal' — Assigns the same weight to every sequence.

multialign(..., 'ScoringMatrix', ScoringMatrixValue) selects the scoring matrix (ScoringMatrixValue) for the progressive alignment. Match and mismatch scores are interpolated from the series of scoring matrices by considering the distances between the two profiles or sequences being aligned. The first matrix corresponds to the smallest distance, and the last matrix to the largest distance. Intermediate distances are calculated using linear interpolation.

multialign(..., 'SMInterp', SMInterpValue), when SMInterpValue is false, turns off the linear interpolation of the scoring matrices. Instead, each supplied scoring matrix is assigned to a fixed range depending on the distances between the two profiles or sequences being aligned.

multialign(..., 'GapOpen', GapOpenValue) specifies the initial penalty for opening a gap.

multialign(..., 'ExtendGap', ExtendGapValue) specifies the initial penalty for extending a gap.

multialign(..., 'DelayCutoff', DelayCutoffValue) specifies a threshold to delay the alignment of divergent sequences whose closest neighbor is farther than

(DelayCutoffValue) * (median patristic distance between sequences)

multialign(..., 'UseParallel', UseParallelValue) specifies whether to use parfor-loops when computing the pairwise alignments. When true, and Parallel Computing Toolbox is installed and a MATLAB pool is open, computation occurs in parallel. If Parallel Computing Toolbox is not installed, or a MATLAB pool is not open, then computation uses parfor-loops in serial mode. Default is false, which uses for-loops in serial mode.

multialign(..., 'Verbose', VerboseValue), when VerboseValue is true, turns on verbosity.

The remaining input optional arguments are analogous to the function profalign and are used through every step of the progressive alignment of profiles.

multialign(..., 'ExistingGapAdjust', ExistingGapAdjustValue), when ExistingGapAdjustValue is false, turns off the automatic adjustment based on existing gaps of the position-specific penalties for opening a gap.

When ExistingGapAdjustValue is true, for every profile position, profalign proportionally lowers the penalty for opening a gap toward the penalty of extending a gap based on the proportion of gaps found in the contiguous symbols and on the weight of the input profile.

multialign(..., 'TerminalGapAdjust', TerminalGapAdjustValue), when TerminalGapAdjustValue is true, adjusts the penalty for opening a gap at the ends of the sequence to be equal to the penalty for extending a gap.

Example 1

Align seven cellular tumor antigen p53 sequences.

p53 = fastaread('p53samples.txt')
ma = multialign(p53,'verbose',true)
showalignment(ma)

Use an UPGMA phylogenetic tree instead as a guiding tree.

dist = seqpdist(p53,'ScoringMatrix',gonnet);
tree = seqlinkage(dist,'UPGMA',p53)

Phylogenetic tree object with 7 leaves (6 branches)

Score the progressive alignment with the PAM family.

ma = multialign(p53,tree,'ScoringMatrix',...
                {'pam150','pam200','pam250'})
showalignment(ma)

Example 2

Enter an array of sequences.

seqs = {'CACGTAACATCTC','ACGACGTAACATCTTCT','AAACGTAACATCTCGC'};

Promote terminations with gaps in the alignment.

multialign(seqs,'terminalGapAdjust',true)

ans =
--CACGTAACATCTC--
ACGACGTAACATCTTCT
-AAACGTAACATCTCGC

Compare the alignment without termination gap adjustment.

multialign(seqs)

ans =
CA--CGTAACATCT--C
ACGACGTAACATCTTCT
AA-ACGTAACATCTCGC

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