SimulateHybridization

SimulateHybridization[oligomer]⟹hybridization

predicts potential secondary structure interactions of the provided list of oligomer.

Details

This function by default conducts Pairing first with the input pair of oligomers, then conducts Folding to infinity depth to allow intra-molecular pairing. If Folding is turned off in option control, only inter-molecular pairing is considered.
The function can also handle a list of oligomer lists as input: SimulateHybridization[{{oligomer..}..}].
Thermodynamic DNA Nearest Neighbor parameters from Object[Report, Literature, "id:kEJ9mqa1Jr7P"]: Allawi, Hatim T., and John SantaLucia. "MeltingCurve and NMR of internal GT mismatches in DNA." Biochemistry 36.34 (1997): 10581-10594.
Thermodynamic RNA Nearest Neighbor parameters from Object[Report, Literature, "id:M8n3rxYAnNkm"]: Xia, Tianbing, et al. "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs." Biochemistry 37.42 (1998): 14719-14735.

Input

Output

General Options

Examples

Basic Examples (5)

When providing a pair of sequences, SimulateHybridization predicts potentially high energy secondary structures the two sequences can form:

SimulateHybridization can return all possible hybridization results even when the input pair of sequences are perfect Waston-Crick reverse complements:

Additionally, SimulateHybridization can handle strands with more than one sequence:

SimulateHybridization can also handle complicate structures:

SimulateHybridization can hybridize multiple input oligomers together, returns all possible intermediate and final structures:

Additional Examples (2)

SimulateHybridization can handle input with a list of oligomer lists:

Return an empty list if two oligomers can not be paired nor can they fold themselves:

Options (16)

Consolidate (2)

If True, return the structures which cannot be further hybridized at current depth:

If False, return all possible intermediate structures which can be further hybridized at current depth:

Depth (2)

Return structures formed by 2 times of recursive hybridizations (including intermediately formed structures):

Return structures formed by exactly 2 times of recursive hybridizations (not including intermediately formed structures):

Folding (2)

If Folding is turned on (by default), will do an interstrand folding to infinity depth after pairing:

If Folding is turned on (by default), will only consider pairing:

MaxMismatch (1)

Maximum number of mismatches allowed in any given duplex:

Method (2)

Sort the returned hybridized structures by ascending energy:

Sort the returned hybridized structures by descending number of bonds:

MinLevel (1)

Specify minimum number of consecutve bases in each hybridization:

MinPieceSize (1)

Minimum number of consecutive paired bases required in a duplex containing mismatches:

Polymer (1)

Specify polymer type:

Temperature (2)

Specify temperature at which hybridization is simulated which will influence the computed free energy:

Template (2)

The options from a previous hybridization simulation (field reference) can be used as a template to create new hybridizations:

The options from a previous hybridization simulation (object) can be used as a template to create new hybridizations:

Messages (1)

InputTooLong (1)

Input can be a maximum of two lists of oligomers. Warning is shown when truncating input to first two inputs: