Detection of Transcription Factor Binding Sites Through Differential Renyi Entropy
Write a training matrix in a MEME/MAST format
Probabilities of each nucleotide in the Homo sapiens organism
according to Thakurta et al.
Similarity Score between a Sequence and a PSSM model
Read MEME motifs and consensus sequences
CalculPWM: To calculate Position Weight Matrix
EntropyRATTUS: Given a Transcription factor chooses the model for a specific organism and method.
DivergenceMUS: Given a Transcription factor chooses the model for a specific organism and method.
A set of initial conditions
Standard output detector
Output MDscan method
Joint Probability
CalculRedundancy: To calculate the redundancy
Library of entropy values
Match algorithm to detect TFBS in a sequence
To create Model Divergence
Library of PredictDivergence values
Run and read MDscan on validation
MATCH algorithm to detect TFBS in a sequence
MEME algorithm to detect TFBS in a sequence
EntropyMUS: Given a Transcription factor chooses the model for a specific organism and method.
Q-residuals detection of TFBS, using a principal components model
Logodds matrix
DivergenceDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method.
Information content in each position of a set of aligned DNA sequences
To read Entropy values
QresidualsMUS: Given a Transcription factor chooses the model for a specific organism and method.
Convert a DNA sequence in a numerical DNA matrix
Multiple sequence alignment by means of ClustalW
DivergenceRATTUS: Given a Transcription factor chooses the model for a specific organism and method.
To create Detection Model
Multiple sequence alignment by means of Muscle (MUltiple Sequence Comparison by Log-Expectation)
PCA model for a set of TFBS
Read nucleotide sequences
Correction entropy from the Finite Sample Size Effect
Renyi Entropy
PCA
A sequence with binding evidence.
A set of Models for the detection
MATCH validation process
To create Model Entropy
Background joint probability
Q to Jackson: transform a Q-residual into a confidence interval
Divergencia.Shannon: Mutual Information
EntropyDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method.
Renyi divergence
Detection: A set of functions for detection of TFBS
Correction of the Finite Sample Size Effect
JacksonParameters: To calculates the parameters needed to transform a Q-residual to a confidence interval
Renyi Order
To create Model transMEME
classMODEL: To choose the model
Conversion of nucleotides to numerical vectors
MDscan algorithm to detect TFBS in a sequence
EntropyHOMO: Given a Transcription factor chooses the model for a specific organism and method.
MDscan algortihm to detect TFBS within a sequence
QresidualsRATTUS: Given a Transcription factor chooses the model for a specific organism and method.
Probability for each nucleotide according to different
organism
Probabilities of each nucleotide in the Homo sapiens organism
according to Thakurta et al.
Detection of Transcription Factor Binding Sites Through Parametric PredictDivergence
DivergenceHOMO: Given a Transcription factor chooses the model for a specific organism and method.
Correction Entropy Approximate from the Finite Sample Size Effect.
A set of functions for detection of Transcription Factor Binding Sites by means of Divergence
The measurement of the variation of the total redundancy
Read output mast
To choose the best paramater for a model
MEME algortihm to detect TFBS within a sequence
Correction redundancy from the Finite Sample Size Effect
Shannon Entropy
Leave-one-out cross-validation for MEME/MAST through training.matrix aligned with MUSCLE or CLUSTALW.
MEME format to training matrix
Multiple sequence alignment by means of MEME.
MAST algorithm to detect TFBS in a sequence
To read PredictDivergence values
Probability
Consensus Sequence for a DNA motif
Leave-one-out cross-validation for MEME
Correction for finite sample effect
Position Specific Scoring Matrices from a set of aligned sequences
PredictEntropy: Detection of Transcription Factor Binding Sites by means of Renyi entropy
Leave-one-out cross-validation for MDscan.
Calcul Score of a Sequence, using a loggods matrix
To calculate redundancy
QresidualsHOMO: Given a Transcription factor chooses the model for a specific organism and method.
PC analysis on numerical DNA sequences
To detect Transcription Factor Binding sites by means of a model
To line up Transcription Factor Binding sites through Multiple Sequence Alignment (MSA)
A set of functions for training of motif discovery algorithms.
Leave-one-out cross-validation for parametric divergence (ITEME).
To calculate joint entropy
QresidualsDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method.
Detection of Transcription Factor Binding Sites Through Parametric PredictDivergence
A set of aligned binding sites sequences
Writes the results of a MEET detection to HTML.
MEET: Motif Elements Estimation Toolkit
P value
Leave-one-out cross-validation for Renyi entropy (ITEME)
ChooseModel: Choose the best model