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The Mycoplasma promoter matrix


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  1. Overview.
  2. Program usage and options.
  3. On the following page you will find a web-based user interface for the matrix program. It allows you to set all relevant options as well as run the program on all data.

    Available options:

    sequence set to use
    You can either choose one of the sequence sets used in [reference] or probe own sequences. To scan your own sequence choose "Alternative sequence" from the pull-down menu and copy your sequence in the provided input field. Note that the sequence must be in fasta or multiple fasta format.
    matrix set to use
    The two provided matrices are ecoli, the original E. coli matrix from Hertz' work [reference], and mpneu, the M. pneumoniae matrix described in [reference]. You can also choose "alternative matrix" and enter your own matrix in the "alternative matrix" input field at the bottom of the page.
    GC content
    The matrix scores are defined as log10(fo/fe), where fe is the expected, and fo the observed nucleotide frequency. Of course, fe depends on the GC content. The GC value should therefore be adjusted to the GC content of the probed sequences. In Mycoplasma pneumoniae, the GC content of putative promoter regions (that is, 100 bases upstream of the ATG) is about 36 %.
    use gap penalties
    Determines whether you want to use the gap penalty. Gap penalties improve promoter detection. However, for the computation of a novel matrix based on experimentally determined promoters it is better to ignore the gap penalties.
    gap limits
    Set the allowed limits for the gap between the +1 and -10 regions, and for the gap between the -10 and -35 regions.
    assume that the promoters are experimentally defined
    Normally, the matrix tries to find the transcription start and +1 region as well as the -10 and -35 regions. However, this makes no sense if the probed sequences have experimentally defined transcription starts. If you check this option, the matrix program will assume that the transcription starts at the 11th base counting from the 3' end of the sequence (sequence downstream from the transcription start is requiered for the computation of a new matrix)
    use a treshold value
    Only putative promoters scoring above the treshold will be shown and taken into account when computating a new matrix.
    print out debugging information
    In case of any problems, switching this option can help to pin down the cause.

  4. References.






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