- Program usage and options.
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
- 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
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
- print out debugging information
- In case of any problems,
switching this option can help to pin down the cause.