|
RNAlib-2.2.5
|
Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):Functions | |
| float | vrna_alifold (const char **ssequences, char *structure) |
| Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA sequence alignment using a comparative method. More... | |
| float | vrna_circalifold (const char **ssequences, char *structure) |
| Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence alignment of circular RNAs using a comparative method. More... | |
| float | alifold (const char **strings, char *structure) |
| Compute MFE and according consensus structure of an alignment of sequences. More... | |
| float | circalifold (const char **strings, char *structure) |
| Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. More... | |
| void | free_alifold_arrays (void) |
| Free the memory occupied by MFE alifold functions. More... | |
| float vrna_alifold | ( | const char ** | ssequences, |
| char * | structure | ||
| ) |
#include <ViennaRNA/alifold.h>
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA sequence alignment using a comparative method.
This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary structure for an RNA sequence alignment using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.
| sequences | RNA sequence alignment |
| structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
| float vrna_circalifold | ( | const char ** | ssequences, |
| char * | structure | ||
| ) |
#include <ViennaRNA/alifold.h>
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence alignment of circular RNAs using a comparative method.
This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary structure for an RNA sequence alignment using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.
Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [6] for further details.
| sequences | Sequence alignment of circular RNAs |
| structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
| float alifold | ( | const char ** | strings, |
| char * | structure | ||
| ) |
#include <ViennaRNA/alifold.h>
Compute MFE and according consensus structure of an alignment of sequences.
This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.
Sufficient space must be allocated for 'structure' before calling alifold().
| strings | A pointer to a NULL terminated array of character arrays |
| structure | A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) |
| float circalifold | ( | const char ** | strings, |
| char * | structure | ||
| ) |
#include <ViennaRNA/alifold.h>
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear.
| strings | A pointer to a NULL terminated array of character arrays |
| structure | A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) |
| void free_alifold_arrays | ( | void | ) |
#include <ViennaRNA/alifold.h>
Free the memory occupied by MFE alifold functions.