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RNAlib-2.2.7
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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_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. More... | |
| 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:
Data Fields | |
| unsigned | i |
| nucleotide position i | |
| unsigned | j |
| nucleotide position j | |
| float | p |
| Probability. | |
| float | ent |
Pseudo entropy for . | |
| short | bp [8] |
| Frequencies of pair_types. | |
| char | comp |
| 1 iff pair is in mfe structure | |
| typedef struct vrna_pinfo_s pair_info |
| 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
| vc | The vrna_fold_compound_t of type VRNA_VC_TYPE_ALIGNMENT with precomputed partition function matrices |
| structure | An optional structure in dot-bracket notation (Maybe NULL) |
| threshold | Do not include results with pair probabilities below threshold |