aacount
Count amino acids in sequence
Syntax
AAStruct
=
aacount(SeqAA
)
AAStruct
= aacount(SeqAA
,
...'Ambiguous', AmbiguousValue
, ...)
AAStruct
= aacount(SeqAA
,
...'Gaps', GapsValue
, ...)
AAStruct
=
aacount(SeqAA
, ...'Chart', ChartValue
,
...)
Input Arguments
| One of the following:
Examples: |
AmbiguousValue | Character vector or string specifying how to treat ambiguous amino acid characters
(
|
GapsValue | Specifies whether gaps, indicated by a hyphen ( |
ChartValue | Character vector or string specifying a chart type. Choices are 'pie' or
'bar' . |
Output Arguments
AAStruct | 1-by-1 MATLAB structure containing fields for the standard
20 amino acids (A , R , N , D , C , Q , E , G , H , I , L , K , M , F , P , S , T , W , Y ,
and V ). |
Description
counts the number
of each type of amino acid in AAStruct
=
aacount(SeqAA
)SeqAA
, an
amino acid sequence, and returns the counts in AAStruct
,
a 1-by-1 MATLAB structure containing fields for the standard
20 amino acids (A
, R
, N
, D
, C
, Q
, E
, G
, H
, I
, L
, K
, M
, F
, P
, S
, T
, W
, Y
,
and V
).
Ambiguous amino acid characters (
B
,Z
, orX
), gaps, indicated by a hyphen (-
), and end terminators (*
) are ignored by default.Unrecognized characters are ignored and cause the following warning message.
Warning: Unknown symbols appear in the sequence. These will be ignored.
calls AAStruct
= aacount(SeqAA
,
...'PropertyName
', PropertyValue
,
...)aacount
with optional properties
that use property name/property value pairs. You can specify one or
more properties in any order. Each PropertyName
must
be enclosed in single quotation marks and is case insensitive. These
property name/property value pairs are as follows:
specifies
how to treat ambiguous amino acid characters (AAStruct
= aacount(SeqAA
,
...'Ambiguous', AmbiguousValue
, ...)B
, Z
,
or X
). Choices are:
'ignore'
(default)'bundle'
'prorate'
'individual'
'warn'
specifies
whether gaps, indicated by a hyphen (AAStruct
= aacount(SeqAA
,
...'Gaps', GapsValue
, ...)-
), are counted
or ignored. Choices are true
or false
(default).
creates a chart showing the relative proportions of
the amino acids. AAStruct
=
aacount(SeqAA
, ...'Chart', ChartValue
,
...)ChartValue
can be 'pie'
or 'bar'
.
Examples
Version History
Introduced before R2006a
See Also
aminolookup
| atomiccomp
| basecount
| codoncount
| dimercount
| isoelectric
| molweight
| proteinplot
| proteinpropplot
| seqviewer