tom-tom

Usage: tom-tom [options] -query <query motifs> -target <target motifs>

Description:

The tom-tom program searches one or more query motifs against a database of target motifs, and reports for each query a list of target motifs, ranked by E-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, tom-tom 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 an E-value. The reported E-value is the minimal E-value over all possible offsets.

Input:

Output:

tom-tom prints to standard output a tab-delimited text file. The file begins with a header, indicated by leading "#" characters. This is followed by a single title line, and then the actual values. The columns are:

The E-value is the expected number of times that a similarity this strong would be observed by chance in a target database of random motifs. 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 E-value.

Options:

Bugs: none known.

Future enhancements:


Authors: Shobhit Gupta (shobhitg@u.washington.edu), Charles E. Grant (cegrant@gs.washington.edu), William Noble (noble@gs.washington.edu)

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