- Installation and Configuration describes how to install and configure
RNAlib
for your requirements
- HelloWorld presents some small example programs to get a first impression on how to use this library
- HelloWorld (Perl/Python) contains small examples that show how to use RNAlib even without C/C++ programming skills from within your favorite scripting language
The model details data structure and its corresponding modifiers.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:214
Various utility- and helper-functions for sequence alignments and comparative structure prediction.
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
Functions for comparative structure prediction using RNA sequence alignments.
char * vrna_random_string(int l, const char symbols[])
Create a random string using characters from a specified symbol set.
void vrna_init_rand(void)
Initialize seed for random number generator.
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:181
float p
Probability of the element.
Definition: structures.h:456
General utility- and helper-functions used throughout the ViennaRNA Package.
void vrna_md_set_default(vrna_md_t *md)
Apply default model details to a provided vrna_md_t data structure.
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence.
General utility- and helper-functions for RNA sequence and structure strings used throughout the Vien...
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
float vrna_pf_fold(const char *sequence, char *structure, vrna_ep_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative met...
#define VRNA_OPTION_DEFAULT
Option flag to specify default settings/requirements.
Definition: fold_compound.h:346
float vrna_alifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
float vrna_mfe(vrna_fold_compound_t *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence,...
MFE calculations for single RNA sequences.
int i
Start position (usually 5' nucleotide that starts the element, e.g. base pair)
Definition: structures.h:454
Partition function implementations.
vrna_fold_compound_t * vrna_fold_compound(const char *sequence, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences.
The Basic Fold Compound API.
int j
End position (usually 3' nucleotide that ends the element, e.g. base pair)
Definition: structures.h:455
void * vrna_alloc(unsigned size)
Allocate space safely.