CalculSimilarity: Similarity Score between a Sequence and a PSSM model

In MEET: MEET: Motif Elements Estimation Toolkit

Description

The Similarity between a Sequence and a PSSM model is calculated using the score of the Sequence, and the minimum and maximum scores that can be obtained with the model. As the score approaches to 1, the sequence is more likely to belong to the modeled motif

Usage

CalculSimilarity(current, minim, maxim)

Arguments

current	Score of the studied sequence
minim	minimum score obtained using the PSSM model
maxim	maximum score obtained using the PSSM model

Value

similarity: between 0 and 1, similarity of the given sequence to the model

Author(s)

Erola Pairo <[e-mail]>

References

A.E. Kel , E. Gossling , I. Reuter , E. Cheremushkin , O.V. Kel-Margoulis , and E. Wingender MATCHTM: a tool for searching transcription factor binding sites in DNA sequences Nucl. Acids Res. 31: 3576-3579.

Examples

require("MEET")
data(TFlogodds)
data(BackgroundOrganism)
data(Sequence)
current<-CalculScores(Sequence, TFlogodds)

maxim<-0
minim<-0

for(j in 1:dim(TFlogodds)[1]){
	  minim <- min(TFlogodds[j,])+minim
	  maxim <- max(TFlogodds[j,])+maxim
	  }
Similarity<-CalculSimilarity(current, minim, maxim)
  

MEET documentation built on May 2, 2019, 1:45 p.m.