RNAlib-2.2.7
Various utilities for Sequence Alignments, and Comparative Structure Prediction
+ Collaboration diagram for Various utilities for Sequence Alignments, and Comparative Structure Prediction:

Files

file  aln_util.h
 Various utility- and helper-functions for sequence alignments and comparative structure prediction.
 

Data Structures

struct  vrna_pinfo_s
 A base pair info structure. More...
 

Typedefs

typedef struct vrna_pinfo_s vrna_pinfo_t
 Typename for the base pair info repesenting data structure vrna_pinfo_s.
 
typedef struct vrna_pinfo_s pair_info
 Old typename of vrna_pinfo_s. More...
 

Functions

vrna_pinfo_tvrna_aln_pinfo (vrna_fold_compound_t *vc, const char *structure, double threshold)
 Retrieve an array of vrna_pinfo_t structures from precomputed pair probabilities. More...
 

Detailed Description


Data Structure Documentation

struct vrna_pinfo_s

A base pair info structure.

For each base pair (i,j) with i,j in [0, n-1] the structure lists:

  • its probability 'p'
  • an entropy-like measure for its well-definedness 'ent'
  • the frequency of each type of pair in 'bp[]'
    • 'bp[0]' contains the number of non-compatible sequences
    • 'bp[1]' the number of CG pairs, etc.

Data Fields

unsigned i
 nucleotide position i
 
unsigned j
 nucleotide position j
 
float p
 Probability.
 
float ent
 Pseudo entropy for $ p(i,j) = S_i + S_j - p_ij*ln(p_ij) $.
 
short bp [8]
 Frequencies of pair_types.
 
char comp
 1 iff pair is in mfe structure
 

Typedef Documentation

typedef struct vrna_pinfo_s pair_info

#include <ViennaRNA/aln_util.h>

Old typename of vrna_pinfo_s.

Deprecated:
Use vrna_pinfo_t instead!

Function Documentation

vrna_pinfo_t* vrna_aln_pinfo ( vrna_fold_compound_t vc,
const char *  structure,
double  threshold 
)

#include <ViennaRNA/aln_util.h>

Retrieve an array of vrna_pinfo_t structures from precomputed pair probabilities.

This array of structures contains information about positionwise pair probabilies, base pair entropy and more

See also
vrna_pinfo_t, and vrna_pf()
Parameters
vcThe vrna_fold_compound_t of type VRNA_VC_TYPE_ALIGNMENT with precomputed partition function matrices
structureAn optional structure in dot-bracket notation (Maybe NULL)
thresholdDo not include results with pair probabilities below threshold
Returns
The vrna_pinfo_t array