| Bioinformatics Toolbox™ | |
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 | String specifying the sequence alphabet. Choices are:
When Alphabet is 'none', the symbol list is based on the observed symbols. Each character can be any symbol, except for a hyphen (-) and a period (.), which are reserved for gaps. |
| CountsValue | Controls returning frequency (ratio of counts/total counts) or counts. Choices are true (counts) or false (frequency). Default is false. |
| GapsValue | String that controls the counting of gaps in a sequence. Choices are:
|
| AmbiguousValue | Controls counting ambiguous symbols. Enter 'Count' to add partial counts to the standard symbols. |
| LimitsValue | Specifies whether to use part of the sequence. Enter a [1x2] vector with the first position and the last position to include in the profile. Default is [1,SeqLength]. |
Profile = seqprofile(Seqs) returns 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
[Profile, Symbols] = seqprofile(Seqs) returns Symbols, a unique symbol list where every symbol in the list corresponds to a row in Profile, the profile.
seqprofile(Seqs, ...'PropertyName', PropertyValue, ...) calls 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(Seqs,
...'Alphabet', AlphabetValue, ...) selects
a nucleotide alphabet, amino acid alphabet, or no alphabet.
seqprofile(Seqs, ...'Counts', CountsValue, ...) when Counts is true, returns the counts instead of the frequency.
seqprofile(Seqs, ...'Gaps', GapsValue, ...) appends a row to the bottom of a profile (Profile) with the count for gaps.
seqprofile(Seqs, ...'Ambiguous', AmbiguousValue, ...) when 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(Seqs, ...'Limits', LimitsValue, ...) specifies the start and end positions for the profile relative to the indices of the multiple alignment.
seqs = fastaread('pf00002.fa');
[P,S] = seqprofile(seqs,'limits',[50 60],'gaps','all')Bioinformatics Toolbox functions: fastaread, multialignread, multialignwrite, seqconsensus, seqdisp, seqlogo
| seqpdist | seqrcomplement | |
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