MEET (version 5.1.1)

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

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

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)