CalculSimilarity: Similarity Score between a Sequence and a PSSM model
In MEET: MEET: Motif Elements Estimation Toolkit

Description Usage Arguments Value Author(s) References See Also Examples

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

1	CalculSimilarity(current, minim, maxim)

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

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

Erola Pairo <epairo@ibecbarcelona.eu>

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.

CalculScores

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)