Tomtom Gps Manual

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Aug 3, 2024, 5:02:18 PM8/3/24

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Tomtom searches one or more query motifs against one or more databases of target motifs (and their reverse complements when applicable), and reports for each query a list of target motifs, ranked by p-value. The E-value and the q-value of each match is also reported. 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.

For a given pair of motifs, the program considers all offsets between the motifs, 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. Columns in the query motif that don't overlap the target motif are assigned a score equal to the median score of the set of random matches to that column.

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 query motif file 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. To compensate for multiple testing, each reported p-value is converted to an E-value by multiplying it by twice the number of target motifs. As a second type of multiple-testing correction, q-values for each match are computed from the set of p-values and reported.

The following command searches query motifs (query.meme) against known motifs provided by CIS-BP (CIS-BP_2.00/Homo_sapiens.meme). It uses pearson correlation (specified by -dist) as the scoring function and only report hits with significance scores higher than 0.1 (specified by -thresh). The output will be written into ./tomtom (specified by -oc), and if the folder exists, old contents will be replaced.

A file containing one or more motifs in MEME format or the HTML (.html) or plain text (.txt) output of MEME or DREME. Each of these motifs will be searched against the target databases. If you only wish to search with a subset of these motifs then look into the -m and -mi options.

File(s) containing MEME formatted motifs. Outputs from MEME and DREME are supported, as well as Minimal MEME Format. You can convert many other motif formats to MEME format using conversion scripts available with the MEME Suite.

The main output file is named tomtom.html and can be viewed with a web browser. The tomtom.html file is created from the tomtom.xml file. An additional file, tomtom.txt, contains a simplified, text-only version of the output. (See -text, below, for the text output format.)

For each query-target match, two additional files containing LOGO alignments may also be written -- an encapsulated postscript file (.eps) if the -eps flag is specified and a portable network graphic file (.png) if the -png flag is specified. An install of ghostscript is required to create the png file.

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