pam
Return Point Accepted Mutation (PAM) scoring matrix
Description
returns the PAMScoringMatrix
= pam(N
)N
scoring matrix for amino acid sequences.
[
returns a structure with information about the PAM matrix.ScoringMatrix
,MatrixInfo
] = pam(N
)
pam(
specifies additional options using one or more name-value arguments.N
,Name=Value
)
Examples
Return the PAM50 Matrix
Use the pam function to return the PAM50 matrix.
PAM50 = pam(50);
Return the PAM250 matrix, and specify the order of amino acids in the matrix.
PAM250 = pam(250,'Order','CSTPAGNDEQHRKMILVFYW');
Input Arguments
N
— Specification of PAM scoring matrix
10 | 20 | 30 | 40 | 50 | 60 | ... | 470 | 480 | 490 | 500
Specification of PAM scoring matrix to return, represented as an integer.
N
accepts integer values starting from 10, and ending at 500 in
increments of 10, only. Hence, 270 is a valid input, but not 275.
Tip
Entering a larger value for N
allows for sequence alignments
with larger evolutionary distances.
Example: 450
Data Types: integer
Name-Value Arguments
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: pam(10,Extended=true)
returns ambiguous characters:
B
,Z
,X
, and the stop character
*
.
Extended
— Flag to return ambiguous characters
false
or 0
(default) | true
or 1
Flag to return of ambiguous characters: B, Z, and X, and the stop character *, in
addition to the 20 standard amino acid characters, specified as a numeric or logical
true
(1) or false
(0).
Data Types: logical
Order
— Order of amino acids in scoring matrix
"ARNDCQEGHILKMFPSTWYVBZX*"
(default) | character vector | string scalar | ...
Order of amino acids in the scoring matrix, specified as a character vector or string scalar. The input string must be of length 20 at least, with each member of the string representing each of the standard 20 amino acids.
If Order
does not contain the ambiguous characters
B
,Z
, X
, or
*
, then these characters are not returned.
You can rearrange the input string in any order, provided the standard 20 amino acids are present.
Example: "QEGCRANDHILKMFPSTWYV"
Data Types: char
| string
Output Arguments
ScoringMatrix
— PAMN
scoring matrix for amino acid sequences
numeric array
PAMN
scoring matrix for amino acid
sequences, returned as an array of integer values.
MatrixInfo
— Information about PAMN
matrix
structure
Information about PAMN
matrix, returned as a
structure. These are the fields of the structure: Name
,
Scale
, Entropy
,
ExpectedScore
, LowestScore
,
HighestScore
, and Order
.
For example, PAM50
scoring matrix has the following values.
struct with fields: Name: 'PAM50' Scale: 0.5000 Entropy: 2 ExpectedScore: -3.7000 LowestScore: -13 HighestScore: 13 Order: 'ARNDCQEGHILKMFPSTWYVBZX*'
Version History
Introduced before R2006a
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