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Calculate sequence properties of DNA oligonucleotide
SeqProperties = oligoprop(SeqNT)
SeqProperties = oligoprop(SeqNT,
...'Salt', SaltValue, ...)
SeqProperties = oligoprop(SeqNT,
...'Temp', TempValue, ...)
SeqProperties = oligoprop(SeqNT,
...'Primerconc', PrimerconcValue, ...)
SeqProperties = oligoprop(SeqNT,
...'HPBase', HPBaseValue, ...)
SeqProperties = oligoprop(SeqNT,
...'HPLoop', HPLoopValue, ...)
SeqProperties = oligoprop(SeqNT,
...'Dimerlength', DimerlengthValue, ...)
SeqNT  DNA oligonucleotide sequence represented by any of the following:

SaltValue  Value that specifies a salt concentration in moles/liter for melting temperature calculations. Default is 0.05 moles/liter. 
TempValue  Value that specifies the temperature in degrees Celsius for nearestneighbor calculations of free energy. Default is 25 degrees Celsius. 
PrimerconcValue  Value that specifies the concentration in moles/liter for melting temperature calculations. Default is 50e6 moles/liter. 
HPBaseValue  Value that specifies the minimum number of paired bases that form the neck of the hairpin. Default is 4 base pairs. 
HPLoopValue  Value that specifies the minimum number of bases that form the loop of a hairpin. Default is 2 bases. 
DimerlengthValue  Value that specifies the minimum number of aligned bases between the sequence and its reverse. Default is 4 bases. 
SeqProperties  Structure containing the sequence properties for a DNA oligonucleotide. 
SeqProperties = oligoprop(SeqNT) returns the sequence properties for a DNA oligonucleotide as a structure with the following fields:
Field  Description 

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  Hbylength(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  Dbylength(SeqNT) matrix of characters displaying all potential dimers for the sequence SeqNT. Each row is a potential dimer of the sequence, with the selfdimerizing 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  4by3 matrix of thermodynamic calculations. The rows correspond to nearestneighbor parameters from: The columns correspond to:

Thermodelta  4by3 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. 
SeqProperties = oligoprop(SeqNT, ...'PropertyName', PropertyValue, ...) calls oligoprop 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:
SeqProperties = oligoprop(SeqNT,
...'Salt', SaltValue, ...) specifies
a salt concentration in moles/liter for melting temperature calculations.
Default is 0.05 moles/liter.
SeqProperties = oligoprop(SeqNT, ...'Temp', TempValue, ...) specifies the temperature in degrees Celsius for nearestneighbor calculations of free energy. Default is 25 degrees Celsius.
SeqProperties = oligoprop(SeqNT, ...'Primerconc', PrimerconcValue, ...) specifies the concentration in moles/liter for melting temperatures. Default is 50e6 moles/liter.
SeqProperties = oligoprop(SeqNT, ...'HPBase', HPBaseValue, ...) specifies the minimum number of paired bases that form the neck of the hairpin. Default is 4 base pairs.
SeqProperties = oligoprop(SeqNT, ...'HPLoop', HPLoopValue, ...) specifies the minimum number of bases that form the loop of a hairpin. Default is 2 bases.
SeqProperties = oligoprop(SeqNT, ...'Dimerlength', DimerlengthValue, ...) specifies the minimum number of aligned bases between the sequence and its reverse. Default is 4 bases.
Calculating Properties for a DNA Sequence
Create a random sequence.
seq = randseq(25) seq = TAGCTTCATCGTTGACTTCTACTAA
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]
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
Calculating Properties for a DNA Sequence with Ambiguous Characters
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]
List the potential dimers for the sequence.
S2.Dimers ans = ACGTagaggacgtn ACGTagaggACGTn acgtagagGACGTN
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[9] http://www.basic.northwestern.edu/biotools/oligocalc.html for weight calculations.