Calculate sequence profile from set of multiply aligned sequences
Profile = seqprofile(Seqs)
[Profile, Symbols]
= seqprofile(Seqs)
seqprofile(Seqs,
...'Alphabet', AlphabetValue, ...)
seqprofile(Seqs,
...'Counts', CountsValue, ...)
seqprofile(Seqs,
...'Gaps', GapsValue, ...)
seqprofile(Seqs,
...'Ambiguous', AmbiguousValue, ...)
seqprofile(Seqs,
...'Limits', LimitsValue, ...)
Seqs | Set of multiply aligned sequences represented by any of the following:.
|
AlphabetValue | Character vector or string specifying the sequence alphabet. Choices are:
When |
CountsValue | Controls returning frequency (ratio
of counts/total counts) or counts. Choices are |
GapsValue | Character vector or string that controls the counting of gaps in a sequence. Choices are:
|
AmbiguousValue | Controls counting ambiguous symbols.
Enter |
LimitsValue | Specifies whether to use part of
the sequence. Enter a |
Profile = seqprofile(Seqs)Profile,
a matrix of size [20 (or 4) x SequenceLength] with
the frequency of amino acids (or nucleotides) for every column in
the multiple alignment. The order of the rows is given by
4 nucleotides — A C G T/U
20 amino acids — A R N D C Q E G H
I L K M F P S T W Y V
[ returns Profile, Symbols]
= seqprofile(Seqs)Symbols,
a unique symbol list where every symbol in the list corresponds to
a row in Profile, the profile.
seqprofile( calls Seqs, ...'PropertyName', PropertyValue,
...)seqprofile 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:
seqprofile( selects
a nucleotide alphabet, amino acid alphabet, or no alphabet.Seqs,
...'Alphabet', AlphabetValue, ...)
seqprofile( when Seqs,
...'Counts', CountsValue, ...)Counts is true,
returns the counts instead of the frequency.
seqprofile( appends
a row to the bottom of a profile (Seqs,
...'Gaps', GapsValue, ...)Profile) with
the count for gaps.
seqprofile( when Seqs,
...'Ambiguous', AmbiguousValue, ...)Ambiguous is 'count',
counts the ambiguous amino acid symbols (B Z X)
and nucleotide symbols (R Y K M S W B D H V N)
with the standard symbols. For example, the amino acid X adds
a 1/20 count to every row while the amino acid B counts
as 1/2 at the D and N rows.
seqprofile( specifies
the start and end positions for the profile relative to the indices
of the multiple alignment.Seqs,
...'Limits', LimitsValue, ...)
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