seqpdist

Calculate pairwise distance between sequences

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Syntax

D = seqpdist(Seqs)
D = seqpdist(Seqs,Name=Value)

Description

D = seqpdist(Seqs) returns the biological distances between each pair of sequences stored in Seqs.

D = seqpdist(Seqs,Name=Value) adjusts aspects of the calculation using name-value arguments.

example

Examples

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Open Live Script

Read amino acid alignment data into a structure.

seqs = fastaread("pf00002.fa");

For every possible pair of sequences in the multiple alignment, ignore sites with gaps and score with the scoring matrix PAM250.

dist = seqpdist(seqs,Method="alignment-score", ...
    Indels="pairwise-delete",...
    ScoringMatrix="pam250");

Force the realignment of each sequence pair ignoring the provided multiple alignment.

dist = seqpdist(seqs,Method="alignment-score",...
    Indels="pairwise-delete", ...
    ScoringMatrix="pam250", ...
    PairwiseAlignment=1);

Measure the Jukes-Cantor pairwise distances after realigning each sequence pair, counting the gaps as point mutations.

dist = seqpdist(seqs,Method="jukes-cantor", ...
    Indels="score", ...
    ScoringMatrix="pam250", ...
    PairwiseAlignment=true);

Input Arguments

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Nucleotide or amino acid sequences, specified as a cell array of character vectors, vector of strings, matrix of characters, or vector of structures.

You can specify:

  • Cell array of character vectors or vector of strings containing nucleotide or amino acid sequences.

  • Matrix of characters, in which each row corresponds to a nucleotide or amino acid sequence.

  • Vector of structures containing a Sequence field.

Name-Value Arguments

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Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: D = seqpdist(Seqs,Method="p-distance") calculates the pairwise distance using the p-distance method.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: D = seqpdist(Seqs,"Method","p-distance")

Method to calculate pairwise distances, specified by a character vector or string scalar in the table.

Methods for Nucleotides and Amino Acids

MethodDescription
p-distance

Proportion of sites at which the two sequences are different. p is close to 1 for poorly related sequences, and p is close to 0 for similar sequences.

d = p

Jukes-Cantor (default)

Maximum likelihood estimate of the number of substitutions between two sequences. p is described with the method p-distance.

For nucleotides:

d = -3/4 log(1-p * 4/3)

For amino acids:

d = -19/20 log(1-p * 20/19)
alignment-score

Distance (d) between two sequences (1, 2) is computed from the pairwise alignment score between the two sequences (score12), and the pairwise alignment score between each sequence and itself (score11, score22) as follows:

d = (1-score12/score11)* (1-score12/score22)
This method does not imply that prealigned input sequences will be realigned, it only scores them. Use with care; this distance method does not comply with the ultrametric condition. In the rare case where the score between sequences is greater than the score when aligning a sequence with itself, then d = 0.

Methods with No Scoring of Gaps (Nucleotides Only)

MethodDescription
Tajima-Nei

Maximum likelihood estimate considering the background nucleotide frequencies.

The seqpdist function can calculate the background nucleotide frequencies from the input sequences. Instead, if you want to specify the nucleotide frequencies, set the OptArgs name-value argument to [gA gC gG gT]. The elements gA, gC, gG, gT are scalar values for the nucleotide frequencies.

KimuraConsiders separately the transitional nucleotide substitution and the transversional nucleotide substitution.
Tamura

Considers separately the transitional nucleotide substitution, the transversional nucleotide substitution, and the GC content.

The seqpdist function can calculate the GC content from the input sequences. Instead, if you want to specify the proportion of GC content, set the OptArgs name-value argument to a numeric scalar in the range [0, 1].

Hasegawa

Considers separately the transitional nucleotide substitution, the transversional nucleotide substitution, and the background nucleotide frequencies.

The seqpdist function can calculate the background nucleotide frequencies from the input sequences. Instead, if you want to specify the nucleotide frequencies, set the OptArgs name-value argument to [gA gC gG gT]. The elements gA, gC, gG, gT are scalar values for the nucleotide frequencies.

Nei-Tamura

Considers separately the transitional nucleotide substitution between purines, the transitional nucleotide substitution between pyrimidines, the transversional nucleotide substitution, and the background nucleotide frequencies.

The seqpdist function can calculate the background nucleotide frequencies from the input sequences. Instead, if you want to specify the nucleotide frequencies, set the OptArgs name-value argument to [gA gC gG gT]. The elements gA, gC, gG, gT are scalar values for the nucleotide frequencies.

Methods with No Scoring of Gaps (Amino Acids Only)

MethodDescription
PoissonAssumes that the number of amino acid substitutions at each site has a Poisson distribution.
Gamma

Assumes that the number of amino acid substitutions at each site has a Gamma distribution with parameter a.

By default, the seqpdist function sets the value of a as 2. Instead, if you want to specify the value of a, set the OptArgs name-value argument to a numeric scalar.

You can also specify a user-defined distance function using @, for example, @distfun. The distance function must have the form:

function D = distfun(S1, S2, OptionalArgs)

The distfun function takes the following arguments:

  • S1 , S2 — Two sequences of the same length (nucleotide or amino acid).

  • OptionalArgs — Optional problem-dependent arguments.

The distfun function returns a scalar that represents the distance between S1 and S2.

Data Types: char | string | function_handle

How to treat sites with gaps, specified as one of these strings or character vectors.

  • score — Scores these sites either as a point mutation or with the alignment parameters, depending on the method selected.

  • pairwise-del — For every pairwise comparison, it ignores the sites with gaps.

  • complete-del — Ignores all the columns in the multiple alignment that contain a gap. This option is available only if you provided a multiple alignment as the input Seqs.

Data Types: char | string

Optional arguments for the distance method, specified as a numeric scalar or a four-element numeric vector.

Methods with No Scoring of Gaps (Nucleotides Only)

MethodDescription
Tajima-NeiBackground nucleotide frequencies, specified as a 4-element numeric vector of the form [gA gC gG gT].
TamuraProportion of GC content, specified as a number in the range [0, 1].
HasegawaBackground nucleotide frequencies, specified as a 4-element numeric vector of the form [gA gC gG gT].
Nei-TamuraBackground nucleotide frequencies, specified as a 4-element numeric vector of the form [gA gC gG gT].

Methods with No Scoring of Gaps (Amino Acids Only)

MethodDescription
GammaShape parameter a of the Gamma distribution, specified as a numeric scalar.

Controls the global pairwise alignment of input sequences, specified as a numeric or logical true (1) or false (0). When true, the seqpdist function performs global pairwise alignment using the nwalign function, while ignoring the multiple alignment of the input sequences (if any).

The default value depends on the length of the sequences:

  • true — When all input sequences do not have the same length.

  • false — When all input sequences have the same length.

Tip

If your input sequences are the same length, then seqpdist assumes they are aligned. If they are not aligned, do one of the following:

  • Align the sequences before passing them to seqpdist, for example, using the multialign function.

  • Set PairwiseAlignment to true when using seqpdist.

Use parallel computation to calculate the distance, specified as a numeric or logical false (0) or true (1).

  • If true, and Parallel Computing Toolbox™ is installed, then computation occurs using parfor-loops.

    • If a parpool is open, then the computation uses the open parpool and occurs in parallel.

    • If there are no open parpool, but automatic creation is enabled in the Parallel Preferences, then the default pool will be automatically opened and computation occurs in parallel.

    • If there are no open parpool and automatic creation is disabled, then computation uses parfor-loops in serial mode.

  • If Parallel Computing Toolbox is not installed, then computation uses parfor-loops in serial mode.

  • If false, then the computation uses for-loops in serial mode.

Return the output D as a square matrix, specified as a numeric or logical false (0) or true (1).

When true, the seqpdist function converts the output into a square matrix such that D(I,J) denotes the distance between the Ith and Jth sequences. The square matrix is symmetric and has a zero diagonal. Setting Squareform to true is the same as using the squareform function in Statistics and Machine Learning Toolbox™.

Type of sequence, specified as "AA" (amino acid) or "NT" (nucleotide).

Data Types: char | string

Scoring matrix to use for the global pairwise alignment, specified as a character vector, string scalar, or numeric matrix.

You can specify a scoring matrix name. Valid choices are:

  • "BLOSUM50" (default for amino acid sequences)

  • "NUC44" (default for nucleotide sequences). This choice is not supported for amino acid sequences.

  • "BLOSUM62"

  • "BLOSUM30" increasing by 5 up to "BLOSUM90"

  • "BLOSUM100"

  • "PAM10" increasing by 10 up to "PAM500"

  • "DAYHOFF"

  • "GONNET"

Note

The above scoring matrices, provided with the software, also include a scale factor that converts the units of the output score to bits. You can also specify the Scale name-value argument to specify an additional scale factor to convert the output score from bits to another unit.

You can also specify a numeric matrix, such as the one returned by the blosum, pam, dayhoff, gonnet, or nuc44 function.

Note

  • If you use a scoring matrix that you created or was created by one of these scoring matrix functions, the matrix does not include a scale factor. The output score will be returned in the same units as the scoring matrix. You can use the Scale name-value argument to specify a scale factor to convert the output score to another unit.

  • If you need to compile seqpdist into a standalone application or software component using MATLAB® Compiler™, use a matrix instead of a character vector or string for ScoringMatrix.

You can specify this argument only when the Method argument is "alignment-score" or the PairwiseAlignment argument is true.

Scale factor applied to the output distance, specified as a positive number. By default, there is no scaling or change in the units of the output distance. If the scoring matrix information also provides a scale factor, then both are used.

Use this argument to control the units of the output distance.

You can specify this argument only when the Method argument is "alignment-score" or the PairwiseAlignment argument is true.

Penalty for opening a gap in the alignment, specified as a positive integer.

You can specify this argument only when the Method argument is "alignment-score" or the PairwiseAlignment argument is true.

Penalty for extending a gap in the alignment, specified as a positive integer. The default is equal to GapOpen.

You can specify this argument only when the Method argument is "alignment-score" or the PairwiseAlignment argument is true.

Output Arguments

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Biological distance between all pairs of sequences stored in the M elements of Seqs, returned as a numeric row vector or a numeric matrix.

By default, D is a row vector of length 1-by-(M*(M-1)/2). The elements are arranged in the order ((2,1),(3,1),..., (M,1),(3,2),...(M,2),...(M,M-1)). This is the lower-left triangle of the full M-by-M distance matrix. To get the distance between the Ith and the Jth sequences for I > J, use the formula D((J-1)*(M-J/2)+I-J).

When you specify the SquareForm name-value argument as true, D is the full M-by-M distance matrix.

Data Types: double

Extended Capabilities

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Version History

Introduced before R2006a

See Also

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