ntdensity

Plot density of nucleotides along sequence

Syntax

ntdensity(SeqNT)

Density = ntdensity(SeqNT)

ntdensity(SeqNT,Window=WindowValue)

Density = ntdensity(SeqNT,Window=WindowValue)

[Density,HighCG] = ntdensity(___,CGThreshold=CGThresholdValue)

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,Window=WindowValue) and Density = ntdensity(SeqNT,Window=WindowValue) uses a window of length WindowValue for the density calculation.

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

Examples

Density of Nucleotides Along Sequence

Create a random character vector to represent a nucleotide sequence.

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

Plot the density of nucleotides along the sequence.

ntdensity(s)

Input Arguments

SeqNT — Nucleotide sequence

character vector | string | row vector of integers | MATLAB structure containing a Sequence field

Nucleotide sequence, specified as one of these values:

• Character vector or string 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.

Data Types: double | char | string | struct

WindowValue — Window length for the density calculation

length(SeqNT)/20 (default) | positive number

Window length for the density calculation, specified as a positive number.

Data Types: double

CGThresholdValue — Threshold for CG content of SeqNT

5 (default) | positive number

Threshold for CG content of SeqNT, specified as a positive number. When you use this argument, ntdensity returns indices for regions where the CG content of SeqNT is greater than CGThresholdValue.

Data Types: double

Output Arguments

Density — Density of nucleotides A, C, G, and T

structure array

Density of nucleotides A, C, G, and T, returned as a structure array.

HighCG — Indices for regions with high CG content

row vector

Indices for regions with high CG content, returned as a row vector. The ntdensity function returns indices for regions where the CG content of SeqNT is greater than CGThresholdValue.

Version History

Introduced before R2006a