CalculScores
(Package: MEET) :
Calcul Score of a Sequence, using a loggods matrix
Giving a logodds matrix, the Score of a sequence is calculated as the sum of the logodds of each nucleotide at each position of the sequence (equivalent to calculating the probability of each nucleotide at each position)
● Data Source:
CranContrib
● Keywords:
● Alias: CalculScores
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This function calculates the redundancy (order) of a random variable X with N possible states.
● Data Source:
CranContrib
● Keywords:
● Alias: CalculRedundancy
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CalculPWM
(Package: MEET) :
CalculPWM: To calculate Position Weight Matrix
This function calculates the PWM (Position Weigth Matrix) from set of aligned nucleotide sequences.
● Data Source:
CranContrib
● Keywords:
● Alias: CalculPWM
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Calculate a PSSM of a set of DNA aligned sequences, taking into account background probabilities. The output is the logodds matrix.
● Data Source:
CranContrib
● Keywords:
● Alias: CalculPSSM
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CalculInformation
(Package: MEET) :
Information content in each position of a set of aligned DNA sequences
Using as an input the set of aligned DNA sequences, information content in each position is calculated, taking into account background probability for each nucleotide. The first row of the returned sequence is the information in each postion, and the others are the loggods matrix.
● Data Source:
CranContrib
● Keywords:
● Alias: CalculInformation
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Alignment
(Package: MEET) :
To line up Transcription Factor Binding sites through Multiple Sequence Alignment (MSA)
This function, Alignment, lines up Transcription Factor Binding Sites, TFBS, through MSA. There are different kinds of MSA: MEME, Clustalw and Muscle
● Data Source:
CranContrib
● Keywords:
● Alias: Alignment
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DNA sequences are aligned by means of Muscle Version 3.8. (Multiple Sequences Alignment)
● Data Source:
CranContrib
● Keywords:
● Alias: align.muscle
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DNA sequences are aligned by means of MEME Version 4.4.0. (Multiple Expectation-Maximization for Motif Elicitation)
● Data Source:
CranContrib
● Keywords:
● Alias: align.MEME
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align.clustalw
(Package: MEET) :
Multiple sequence alignment by means of ClustalW
DNA sequences are aligned by means of ClustalW (Multiple Sequence Alignment).
● Data Source:
CranContrib
● Keywords:
● Alias: align.clustalw
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writeResultsHTML
(Package: MEET) :
Writes the results of a MEET detection to HTML.
This function writes the results of a MEET detection step into an HTML file.
● Data Source:
CranContrib
● Keywords:
● Alias: writeResultsHTML
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