RNAlib-2.4.17
Getting Started
  • 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
model.h
The model details data structure and its corresponding modifiers.
vrna_elem_prob_s
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
vrna_md_s::gquad
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:214
alignments.h
Various utility- and helper-functions for sequence alignments and comparative structure prediction.
vrna_fold_compound_free
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
alifold.h
Functions for comparative structure prediction using RNA sequence alignments.
vrna_random_string
char * vrna_random_string(int l, const char symbols[])
Create a random string using characters from a specified symbol set.
vrna_init_rand
void vrna_init_rand(void)
Initialize seed for random number generator.
vrna_md_s::temperature
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:181
vrna_elem_prob_s::p
float p
Probability of the element.
Definition: structures.h:456
basic.h
General utility- and helper-functions used throughout the ViennaRNA Package.
vrna_md_set_default
void vrna_md_set_default(vrna_md_t *md)
Apply default model details to a provided vrna_md_t data structure.
vrna_fold
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence.
strings.h
General utility- and helper-functions for RNA sequence and structure strings used throughout the Vien...
vrna_md_s
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
mfe.h
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
vrna_pf_fold
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...
VRNA_OPTION_DEFAULT
#define VRNA_OPTION_DEFAULT
Option flag to specify default settings/requirements.
Definition: fold_compound.h:355
vrna_alifold
float vrna_alifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
vrna_mfe
float vrna_mfe(vrna_fold_compound_t *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence,...
fold.h
MFE calculations for single RNA sequences.
vrna_elem_prob_s::i
int i
Start position (usually 5' nucleotide that starts the element, e.g. base pair)
Definition: structures.h:454
part_func.h
Partition function implementations.
fold_compound.h
The Basic Fold Compound API.
vrna_fold_compound
vrna_fold_compound_t * vrna_fold_compound(const char *sequence, const vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences.
vrna_elem_prob_s::j
int j
End position (usually 3' nucleotide that ends the element, e.g. base pair)
Definition: structures.h:455
vrna_alloc
void * vrna_alloc(unsigned size)
Allocate space safely.