version 1.0

1. Introduction

    Program enoLOGOS generates LOGOs of transcription factor DNA binding sites from various types of input matrices. It can utilize standard count matrices, probability matrices or matrices of "energy" values (i.e., log-frequencies). In the latter case, it will first convert the energy values into probabilities using the Boltzmann distribution, where the probability of base b at position i is defined as:

    The height of the stack of symbols in each position is calculated to be the relative entropy for this position:

    Finally, the height of the stack of individual symbols in each position is calculated to be proportional to their probability in this position.

2. Parameters

  1. Matrix input format: The user can enter the weight matrix in horizontal or vertical format; i.e., the rows will correspond to the base type or the positions of the matrix, respectively. Lines that are preceded by "#" are considered comment lines and are ignored. A single matrix header line starting with "PO" can specify position labels (horizontal matrices) or base types (vertical matrices) of the logo columns. If a matrix header is found, then the first item on each subsequent line will be used as either the base type or position label of the horizontal or vertical matrix, respectively. Examples of horizontal and vertical matrices follow.


  2. Alignment input format: The user can also enter a set of aligned DNA or RNA sequences in the input. In this case the input sequences should be either in FastA format or standard (raw) sequence alignment format. An alignment matrix will be created from the aligned sequences. Any character other than white space in an alignment (e.g., "-", "." or "*") designates insertion. All white space characters are ignored.

    # example sequence alignment
    LABELS = -2 -1 0 +1 +2 +3 +4 +5 +6

  3. Weight type: The user may need to specify the type of data in the weight matrix:
    1. unknown: The program will try to infer the input type as best it can.
    2. energies: Weights will be interpreted as energies and converted to probabilities as defined above.
    3. alignment counts: Counts will be converted to probabilities with the addition of pseudo counts (psi) proportional to the background frequency of the letter/nucleotide, p(b). Each probability is calculated as:
    4. where c is the count of letter b in position i, n is the total number of alignment counts and psi is typically set to 1.
    5. probabilities: Values for each position in the pattern will be normalized to sum to 1.
    6. arbitrary: Weights will be used "as is". To be plotted with LOGO plot method "weights as entered".

  4. Energy units: If the weight type is energies, then the energy units may need to be chosen.
    1. kT: The default.
    2. kcal/mol
    3. kJ/mol
    4. J/mol

  5. LOGO plot method: The user can select the method for calculation of the height of the symbol stacks. The two most popular are Shannon's entropy (also known as information content) and relative entropy (i.e., information content corrected for the background).
    1. relative entropy: H(i) as defined as above. Will generate Shannon's entropy when prior probabilities are equiprobable.
    2. frequency: Letter heights will be generated from their calculated probabilities (heights will sum to 1).
    3. weights as entered: When weight type is set to arbitrary, letter heights will reflect the input weights.

  6. Log base: The user specifies the preferred base for calculation of the logarithms in the final plot.

  7. Title (optional): The user specifies a title to be printed on the top of the plot.

  8. Axis labels (optional): The user specifies whether the labels for the x-axis and y-axis will be printed.

  9. Scale letters by probability: When "ON" (the default), each letter is scaled proportional to its probability where the total height of the column is the relative entropy H(i). When "OFF", letter heights will be proportional to the absolute value of relative entropy contribution for that letter. Note that the latter method will generate LOGOs where the bases with negative relative entropy are plotted upside-down.

  10. Wts (negate): If the energies are negative, then they may be negated with this option (all weights multiplied by -1) .

  11. Y-axis height: The user specifies the maximum height for the y-axis. This can be useful to users that want to print LOGOs of many patterns and want them to be on the same scale for comparison purposes. This value will be reset if the actual column heights exceed this value.

  12. X-axis, Y-axis: Control for turning ON and OFF the plotting of x- and y-axis.

  13. Mutual information: If the input data are aligned sequence (stack of sites or in FastA format), then the mutual information can be calculated and displayed for each pair of alignment positions. Mutual information is the relative entropy between a joint distribution (in our case, the two columns under comparison) and the product distribution (of the independent columns).

  14. Aspect ratio: This option allows control over the LOGO column height-to-width aspect ratio. The default of 3, means that the height of the tallest column is 3 times the letter width. Typically this will need to be increased when the total number of positions exceeds 20 and decreased when the number of positions is less than about 6.

  15. Symbol colors: The user specifies the color of each symbol using the RGB system.

  16. %GC: The user specifies the reference probabilities for the four bases in terms of %GC content. E.g., for an organism with 40% GC, p(A)=p(T)=0.3 and p(C)=p(G)=0.2.

3. Reference