CalculPSSM: Position Specific Scoring Matrices from a set of aligned...

In MEET: MEET: Motif Elements Estimation Toolkit

Description

Calculate a PSSM of a set of DNA aligned sequences, taking into account background probabilities. The output is the logodds matrix.

Usage

CalculPSSM(matriu, Prob)

Arguments

matriu	Set of DNA aligned sequences
Prob	Probability distribution of the nucleotides in the background model

Value

logodds: logodds matrix calculated as a log2 of the frequency matrix

Author(s)

Erola Pairo <epeiroatibec.pcb.ub.es>

References

Gary D. Stormo. DNA binding sites: representation and discovery. Bioinformatics (2000) 16(1): 16-23 doi:10.1093/bioinformatics/16.1.16

See Also

CalculInformation

Examples

data(TranscriptionFactor)
data(BackgroundOrganism)
CalculPSSM(matriu=TranscriptionFactor, Prob=Prob)

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