Tomtom is a tool for comparing a DNA motif to a database of known motifs.
The Tomtom web application compares an input DNA motif to the elements of a
database of known motifs (and their DNA reverse complements).
A list of matching motifs is reported, ranked by q-value.
The q-value is the minimal false discovery rate at which the observed
similarity would be deemed significant. The output contains
results for each query, in the order that the queries appear in
the input file. With respect to each query, targets are ranked
by q-value.
For a given pair of motifs, the program considers all offsets,
while requiring a minimum number of overlapping positions. For a
given offset, each overlapping position is scored using one of
seven column similarity functions defined below. In order to
compute the scores, Tomtom needs to know the
frequencies of the letters of the sequence alphabet in the
database being searched (the "background" letter
frequencies). By default, the background letter frequencies
included in the MEME input files are used. The scores of columns
that overlap for a given offset are summed. This summed score is
then converted to a p-value. The reported p-value is the minimal
p-value over all possible offsets. For each query motif, the
corresponding p-values are then converted to q-values.
Required Tomtom Inputs
Three inputs must be provided on the Tomtom web page:
A single DNA motif, with each column showing the counts
of bases A, C, G, and T, in that position of the motif.
The motif is pasted into the text box labeled "Paste your DNA here".
The DNA motif database to search.
This is selected from the drop-down list labeled "Select the DNA Motif
Database to Search".
The function used to compare motifs.
This is selected from the drop-down list labeled "Select the Motif Column
Comparison Function".
The contents of the required fields can be cleared by clicking
on the "Clear Input" button.
Submitting a Tomtom job
After filling in the required inputs on the Tomtom web page
the job can be submitted for processing by clicking on the "Start Search" button.
Alternatively, if you have no motif and would just like to see sample Tomtom output,
you can just select the DNA motif databse, the motif column comparison function
and then click on the "Search with Example Motif" button.
Totom output
The result of submitting your job will be a page that displays the
status of your job on the Tomtom server, and contains a link to your Tomtom
results. The output of Tomtom is a web page displaying a table of motifs
in the database similar to the motif you submitted (sample Tomtom
output). Each entry in the table
includes the database identifier for matching motif, its description, the
p-value and q-value of the match, the overlap and offset between your motif
and the matching motif, the strand of the matching motif, and a logogram
of your motif and the matching motif.
