RNAlib-2.3.1
aln_util.h File Reference

Various utility- and helper-functions for sequence alignments and comparative structure prediction. More...

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Data Structures

struct  vrna_pinfo_s
 A base pair info structure. More...
 
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...
 
int vrna_aln_mpi (const char **alignment)
 Get the mean pairwise identity in steps from ?to?(ident) More...
 
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...
 
int get_mpi (char *Alseq[], int n_seq, int length, int *mini)
 Get the mean pairwise identity in steps from ?to?(ident) More...
 
void encode_ali_sequence (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)
 Get arrays with encoded sequence of the alignment. More...
 
void alloc_sequence_arrays (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)
 Allocate memory for sequence array used to deal with aligned sequences. More...
 
void free_sequence_arrays (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)
 Free the memory of the sequence arrays used to deal with aligned sequences. More...
 

Detailed Description

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

Typedef Documentation

typedef struct vrna_pinfo_s pair_info

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 
)

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_FC_TYPE_COMPARATIVE 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