# oligoprop

Calculate sequence properties of DNA oligonucleotide

## Syntax

``SeqProperties = oligoprop(SeqNT)``
``SeqProperties = oligoprop(SeqNT,Name,Value)``

## Description

````SeqProperties = oligoprop(SeqNT)` returns the sequence properties for a DNA oligonucleotide as a structure.```

example

````SeqProperties = oligoprop(SeqNT,Name,Value)` uses additional options specified by one or more `Name,Value` pair arguments.```

## Examples

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1. Create a random sequence.

```seq = randseq(25) seq = TAGCTTCATCGTTGACTTCTACTAA```
2. Calculate sequence properties of the sequence.

```S1 = oligoprop(seq) S1 = GC: 36 GCdelta: 0 Hairpins: [0x25 char] Dimers: 'tAGCTtcatcgttgacttctactaa' MolWeight: 7.5820e+003 MolWeightdelta: 0 Tm: [52.7640 60.8629 62.2493 55.2870 54.0293 61.0614] Tmdelta: [0 0 0 0 0 0] Thermo: [4x3 double] Thermodelta: [4x3 double]```
3. List the thermodynamic calculations for the sequence.

```S1.Thermo ans = -178.5000 -477.5700 -36.1125 -182.1000 -497.8000 -33.6809 -190.2000 -522.9000 -34.2974 -191.9000 -516.9000 -37.7863```
1. Calculate sequence properties of the sequence ACGTAGAGGACGTN.

```S2 = oligoprop('ACGTAGAGGACGTN') S2 = GC: 53.5714 GCdelta: 3.5714 Hairpins: 'ACGTagaggACGTn' Dimers: [3x14 char] MolWeight: 4.3329e+003 MolWeightdelta: 20.0150 Tm: [38.8357 42.2958 57.7880 52.4180 49.9633 55.1330] Tmdelta: [1.4643 1.4643 10.3885 3.4633 0.2829 3.8074] Thermo: [4x3 double] Thermodelta: [4x3 double] ```
2. List the potential dimers for the sequence.

```S2.Dimers ans = ACGTagaggacgtn ACGTagaggACGTn acgtagagGACGTN```

## Input Arguments

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DNA oligonucleotide sequence represented by any of the following:

• Character vector or string containing the letters `A`, `C`, `G`, `T`, or `N`

• Vector of integers containing the integers `1`, `2`, `3`, `4`, or `15`

• Structure containing a `Sequence` field that contains a nucleotide sequence

### Name-Value Arguments

Specify optional pairs of arguments as `Name1=Value1,...,NameN=ValueN`, where `Name` is the argument name and `Value` is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: `'Replicates',5` specifies to repeat the algorithm five times.

Specify a salt concentration in moles/liter for melting temperature calculations

Example: `'Salt',0.02`

Specify the temperature in degrees Celsius for nearest-neighbor calculations of free energy.

Example: `'Temp',20`

Specify the concentration in moles/liter for melting temperatures.

Example: `'Primerconc',40e-6`

Specify the minimum number of paired bases that form the neck of the hairpin.

Example: `'HPBase',6`

Specify the minimum number of bases that form the loop of a hairpin.

Example: `'HPLoop',2`

Specify the minimum number of aligned bases between the sequence and its reverse

Example: `'Dimmerlength',6`

## Output Arguments

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Sequence properties for a DNA oligonucleotide as a structure with the following fields:

FieldDescription
`GC`Percent GC content for the DNA oligonucleotide. Ambiguous `N` characters in `SeqNT` are considered to potentially be any nucleotide. If `SeqNT` contains ambiguous `N` characters, `GC` is the midpoint value, and its uncertainty is expressed by `GCdelta`.
`GCdelta`The difference between `GC` (midpoint value) and either the maximum or minimum value `GC` could assume. The maximum and minimum values are calculated by assuming all `N` characters are G/C or not G/C, respectively. Therefore, `GCdelta` defines the possible range of GC content.
`Hairpins``H`-by-`length(SeqNT)` matrix of characters displaying all potential hairpin structures for the sequence `SeqNT`. Each row is a potential hairpin structure of the sequence, with the hairpin forming nucleotides designated by capital letters. `H` is the number of potential hairpin structures for the sequence. Ambiguous `N` characters in `SeqNT` are considered to potentially complement any nucleotide.
`Dimers ``D`-by-`length(SeqNT)` matrix of characters displaying all potential dimers for the sequence `SeqNT`. Each row is a potential dimer of the sequence, with the self-dimerizing nucleotides designated by capital letters. `D` is the number of potential dimers for the sequence. Ambiguous `N` characters in `SeqNT` are considered to potentially complement any nucleotide.
`MolWeight`Molecular weight of the DNA oligonucleotide. Ambiguous `N` characters in `SeqNT` are considered to potentially be any nucleotide. If `SeqNT` contains ambiguous `N` characters, `MolWeight` is the midpoint value, and its uncertainty is expressed by `MolWeightdelta`.
`MolWeightdelta`The difference between `MolWeight` (midpoint value) and either the maximum or minimum value `MolWeight` could assume. The maximum and minimum values are calculated by assuming all `N` characters are `G` or `C`, respectively. Therefore, `MolWeightdelta` defines the possible range of molecular weight for `SeqNT`.
`Tm`

A vector with melting temperature values, in degrees Celsius, calculated by six different methods, listed in the following order:

Ambiguous `N` characters in `SeqNT` are considered to potentially be any nucleotide. If `SeqNT` contains ambiguous `N` characters, `Tm` is the midpoint value, and its uncertainty is expressed by `Tmdelta`.

`Tmdelta`A vector containing the differences between `Tm` (midpoint value) and either the maximum or minimum value `Tm` could assume for each of the six methods. Therefore, `Tmdelta` defines the possible range of melting temperatures for `SeqNT`.
`Thermo`

`4`-by-`3` matrix of thermodynamic calculations.

The rows correspond to nearest-neighbor parameters from:

The columns correspond to:

• delta `H` — Enthalpy in kilocalories per mole, kcal/mol

• delta `S` — Entropy in calories per mole-degrees Kelvin, cal/(K)(mol)

• delta `G` — Free energy in kilocalories per mole, kcal/mol

Ambiguous `N` characters in `SeqNT` are considered to potentially be any nucleotide. If `SeqNT` contains ambiguous `N` characters, `Thermo` is the midpoint value, and its uncertainty is expressed by `Thermodelta`.

`Thermodelta``4`-by-`3` matrix containing the differences between `Thermo` (midpoint value) and either the maximum or minimum value `Thermo` could assume for each calculation and method. Therefore, `Thermodelta` defines the possible range of thermodynamic values for `SeqNT`.

## References

[1] Breslauer, K.J., Frank, R., Blöcker, H., and Marky, L.A. (1986). Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Science USA 83, 3746–3750.

[2] Chen, S.H., Lin, C.Y., Cho, C.S., Lo, C.Z., and Hsiung, C.A. (2003). Primer Design Assistant (PDA): A web-based primer design tool. Nucleic Acids Research 31(13), 3751–3754.

[3] Howley, P.M., Israel, M.A., Law, M., and Martin, M.A. (1979). A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. The Journal of Biological Chemistry 254(11), 4876–4883.

[4] Marmur, J., and Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. Journal Molecular Biology 5, 109–118.

[5] Panjkovich, A., and Melo, F. (2005). Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics 21(6), 711–722.

[6] SantaLucia Jr., J., Allawi, H.T., and Seneviratne, P.A. (1996). Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability. Biochemistry 35, 3555–3562.

[7] SantaLucia Jr., J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Science USA 95, 1460–1465.

[8] Sugimoto, N., Nakano, S., Yoneyama, M., and Honda, K. (1996). Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research 24(22), 4501–4505.

## Version History

Introduced before R2006a