RNAlib-2.4.3
Comparative structure prediction

compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments More...

+ Collaboration diagram for Comparative structure prediction:

Modules

 MFE Consensus Structures for Sequence Alignment(s)
 
 Partition Function and Base Pair Probabilities for Sequence Alignment(s)
 
 Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
 
 Local MFE Consensus Structure Prediction for Sequence Alignments
 

Files

file  alifold.h
 Functions for comparative structure prediction using RNA sequence alignments.
 

Functions

float energy_of_alistruct (const char **sequences, const char *structure, int n_seq, float *energy)
 Calculate the free energy of a consensus structure given a set of aligned sequences. More...
 
int get_alipf_arrays (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)
 Get pointers to (almost) all relavant arrays used in alifold's partition function computation. More...
 
void update_alifold_params (void)
 Update the energy parameters for alifold function. More...
 
float ** get_ribosum (const char **Alseq, int n_seq, int length)
 Retrieve a RiboSum Scoring Matrix for a given Alignment.
 

Variables

double cv_fact
 This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. More...
 
double nc_fact
 This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. More...
 

Detailed Description

compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments

Consensus structures can be predicted by a modified version of the fold() algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see [9] and [2].

Function Documentation

◆ energy_of_alistruct()

float energy_of_alistruct ( const char **  sequences,
const char *  structure,
int  n_seq,
float *  energy 
)

#include <ViennaRNA/alifold.h>

Calculate the free energy of a consensus structure given a set of aligned sequences.

Deprecated:
Usage of this function is discouraged! Use vrna_eval_structure(), and vrna_eval_covar_structure() instead!
Parameters
sequencesThe NULL terminated array of sequences
structureThe consensus structure
n_seqThe number of sequences in the alignment
energyA pointer to an array of at least two floats that will hold the free energies (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term)
Returns
free energy in kcal/mol

◆ get_alipf_arrays()

int get_alipf_arrays ( short ***  S_p,
short ***  S5_p,
short ***  S3_p,
unsigned short ***  a2s_p,
char ***  Ss_p,
FLT_OR_DBL **  qb_p,
FLT_OR_DBL **  qm_p,
FLT_OR_DBL **  q1k_p,
FLT_OR_DBL **  qln_p,
short **  pscore 
)

#include <ViennaRNA/alifold.h>

Get pointers to (almost) all relavant arrays used in alifold's partition function computation.

Note
To obtain meaningful pointers, call alipf_fold first!
See also
pf_alifold(), alipf_circ_fold()
Deprecated:
It is discouraged to use this function! The new vrna_fold_compound_t allows direct access to all necessary consensus structure prediction related variables!
See also
vrna_fold_compound_t, vrna_fold_compound_comparative(), vrna_pf()
Parameters
S_pA pointer to the 'S' array (integer representation of nucleotides)
S5_pA pointer to the 'S5' array
S3_pA pointer to the 'S3' array
a2s_pA pointer to the alignment-column to sequence position mapping array
Ss_pA pointer to the 'Ss' array
qb_pA pointer to the QB matrix
qm_pA pointer to the QM matrix
q1k_pA pointer to the 5' slice of the Q matrix ( $q1k(k) = Q(1, k)$)
qln_pA pointer to the 3' slice of the Q matrix ( $qln(l) = Q(l, n)$)
pscoreA pointer to the start of a pscore list
Returns
Non Zero if everything went fine, 0 otherwise

◆ update_alifold_params()

void update_alifold_params ( void  )

#include <ViennaRNA/alifold.h>

Update the energy parameters for alifold function.

Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like temperature

Deprecated:
Usage of this function is discouraged! The new API uses vrna_fold_compound_t to lump all folding related necessities together, including the energy parameters. Use vrna_update_fold_params() to update the energy parameters within a vrna_fold_compound_t.

Variable Documentation

◆ cv_fact

double cv_fact

#include <ViennaRNA/alifold.h>

This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.

Deprecated:
See vrna_md_t.cv_fact, and vrna_mfe() to avoid using global variables

Default is 1.

◆ nc_fact

double nc_fact

#include <ViennaRNA/alifold.h>

This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.

Deprecated:
See vrna_md_t.nc_fact, and vrna_mfe() to avoid using global variables

Default is 1.