TOMTOM: Search for similar motifs in motif databases Options: -dist (pearson|ed|sandelin) distance function to use; default pearson -ev evalue threshold; default 10; not usable with -qv -qv qvalue threshold; not usable with -ev -m filter query motifs by name (id); repeatable -mi filter query motifs by file order; repeatable -uptargets uploaded target motifs -incomplete_scores don't included unaligned parts of the motif in scoring -niced run tomtom niced -help brief help message Distance Functions pearson - Pearson correlation coefficient ed - Euclidean distance sandelin - Sandelin-Wasserman similarity function Motif Databases The motif databases may be specified as a pattern using * as a wildcard. ]]> incomplete_scores -incomplete_scores false Score only aligned portions dist -dist STRING true pearson ed sandelin pearson Column Comparison Function ev -ev FLOAT 10 E-value qv -qv FLOAT 0.1 q-value mi -mi INT Select by position m -m STRING Select by name uptargets -uptargets FILE INPUT Upload Motif Database queries FILE INPUT true Query Motifs dbtargets STRING Filename of Motif Database queries_in queries Query Motifs filter m mi true Optionally select the query motif (exclusive) targets_in dbtargets uptargets Target Motifs comparison dist incomplete_scores Motif Comparison Options threshold ev qv true true Output Threshold (exclusive) @SERVICE_DIR@/tomtom_webservice false