Bioinformatics Toolbox™

ntdensity - Plot density of nucleotides along sequence

Syntax

ntdensity(SeqNT)
Density = ntdensity(SeqNT, 'PropertyName', PropertyValue)

ntdensity(..., 'Window', WindowValue)
[Density, HighCG] = ntdensity(..., 'CGThreshold', CGThresholdValue)

Description

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

Density = ntdensity(SeqNT, 'PropertyName', PropertyValue) returns a MATLAB^® structure with the density of nucleotides A, C, G, and T.

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

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

Examples

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

See Also

Bioinformatics Toolbox™ functions: basecount, codoncount, cpgisland, dimercount

MATLAB function: filter

nt2int

nuc44