Documentation

ExtinctionCoefficient

ExtinctionCoefficient[n]⟹extinction

determines the extinction coefficent at 260 (nm) of an average sequence of length n.

ExtinctionCoefficient[sequence]⟹extinction

determines the extinction coefficent at 260 (nm) of the provided sequence.

ExtinctionCoefficient[strand]⟹extinction

determine the extinction coefficent at 260 (nm) of the provided strand.

ExtinctionCoefficient[structure]⟹extinction

determine the extinction coefficent at 260 (nm) of the provided structure.

ExtinctionCoefficient[object]⟹extinction

determine the extinction coefficent at 260 (nm) of the provided object.

Details

The Extinction Coefficient calculation is based on the formula as described in Object[Report, Literature, "id:pZx9jon4xKW9"]: V. Bloomfield et al, "Nucleic acids: structures, properties and functions." (2000) p174-176.
For DNA, the extinction coefficient and the hyperchromacity at 260 nm values can be found in Object[Report, Literature, "id:kEJ9mqR5EmJB"]: A. V. Tataurov et al, "Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids." (2008) p66-70.

Input

Output

General Options

Examples

Basic Examples (5)

Compute extinction coefficient of a sequence:

Given a strand:

Given a structure:

Compute extinction coefficient of the Structure in a sample:

Given list of sequence inputs:

Additional Examples (6)

Given RNA sequence:

Peptide input:

Directly pull extinction coefficient from Models:

Strand input:

Given a bonded structure:

Given a structure with two modifications:

Options (4)

Duplex (1)

Also calculate the extinction coefficient of its reverse complement:

ExtinctionCoefficientsModel (1)

Specify a model for extinction coefficient -- In this case extinction coefficients of DNA is used:

Polymer (1)

Specify a polymer type:

Units (1)

If True, the function outputs the unit in mL/(mg cm). If False, the function outputs the regular extinction coefficient unit in L/(cm mol):