Public Attributes

gotoh_motif Struct Reference

Holds the input 2-sided motif. More...

#include <structs.h>

List of all members.

Public Attributes

char * comment
char * name
int nLeft
int nRight
int len
float ** stemL
float ** stemR
float * minL
float * maxL
float * infoL
int * maxCL
char * consL
float * minR
float * maxR
float * infoR
int * maxCR
char * consR
int n_bp
int ** basepairs
float scoreBP
float maxScore

Detailed Description

Holds the input 2-sided motif.

gotoh_motif holds the frequency matrices and the base pair table of a 2-sided motif. Additionally, it stores min, max, information content and consensus as well as maximal possible scores for sequence and structure.


Member Data Documentation

Positions of paired bases in their stems and base pair type. 3 columns:

  • 0 - i (left)
  • 1 - j (right)
  • 2 - type

Comment for the motif, provided in input file.

Base at maxCL - Consensus sequence of left stem.

Base at maxCR - Consensus sequence of left stem.

Information content of stemL.

Information content of stemR.

Minimal length of motif. Default: nLeft + nRight + 3

Number of base at max value in stemL. {0,1,2,3,4} for {A,C,G,U,-}.

Number of base at max value in stemR. {0,1,2,3,4} for {A,C,G,U,-}.

Maximal values of stemL.

Maximal values of stemR.

Complete score of consensus motif: sum((sum(maxL), sum(maxR), scoreBP))

Minimal values of stemL.

Minimal values of stemR.

Number of base pairs.

Name of the motif. So far, same as comment.

The size of the left stem of a 2-sided motif.

The size of the right stem of a 2-sided motif.

Structure score consensus motif

Frequency table of left stem.

Frequency table of right stem.


The documentation for this struct was generated from the following file:
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