ntdensity - Plot density of nucleotides along sequence

Syntax

Arguments

SeqNT	One of the following: String of codes specifying a nucleotide sequence. For valid letter codes, see the table Mapping Nucleotide Letter Codes to Integers. Row vector of integers specifying a nucleotide sequence. For valid integers, see the table Mapping Nucleotide Integers to Letter Codes. MATLAB structure containing a Sequence field that contains a nucleotide sequence, such as returned by emblread, fastaread, fastqread, genbankread, getembl, or getgenbank. Note   Although you can submit a sequence with nucleotides other than A, C, G, and T, ntdensity plots only A, C, G, and T.
WindowValue	Value that specifies the window length for the density calculation. Default is length(SeqNT)/20.
CGThresholdValue	Controls the return of indices for regions where the CG content of SeqNT is greater than CGThresholdValue. Default is 5.

Description

ntdensity(SeqNT) plots the density of nucleotides A, C, G, and T in sequence SeqNT.

Density = ntdensity(SeqNT) returns a MATLAB structure with the density of nucleotides A, C, G, and T.

... = ntdensity(SeqNT, ...'PropertyName', PropertyValue, ...) calls ntdensity 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:

... = ntdensity(..., 'Window', WindowValue, ...) uses a window of length WindowValue for the density calculation. Default WindowValue is length(SeqNT)/20.

[Density, HighCG] = ntdensity(..., 'CGThreshold', CGThresholdValue, ...) returns indices for regions where the CG content of SeqNT is greater than CGThresholdValue. Default CGThresholdValue is 5.

Examples

1. Create a random character string to represent a nucleotide sequence.

   s = randseq(1000, 'alphabet', 'dna');

2. Plot the density of nucleotides along the sequence.

   ntdensity(s)

See Also

basecount | codoncount | cpgisland | dimercount | filter

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