CENTRIMO: Determine which motifs occur centrally in ChIP-seq output. Options: -local compute the enrichment of all regions; default: central regions only -score minimum score counted as hit -optsc search for optimized score above the threshold given by '-score' argument. Slow computation due to multiple tests -ethresh minimum E-value to report -maxreg maximum region size to test -neg plot a negative set of sequences against the default set and test each window with Fisher's Exact Test -upmotifs uploaded motifs -bfile background file (0-order) -norc don't scan with the reverse complement motif -flip allow 'fliping' of sequences causing rc matches to appear 'reflected' around center -noseq don't store sequence ids in the output -help brief help message Motif Databases The motif databases may be specified as a pattern using * as a wildcard. ]]> local -local Localized Search false optsc -optsc Optimize Score false norc -norc No Reverse Complement false flip -flip Reflect RC Matches false noseq -noseq Don't Store Seq IDs false score -score FLOAT 5 Minimum Site Score ethresh -ethresh FLOAT 10 E-value threshold maxreg -maxreg INT Maximum region size to test neg -neg FILE INPUT Comparative Sequences bfile -bfile FILE INPUT Upload Background upmotifs -upmotifs FILE INPUT Upload Motif Database sequences FILE INPUT true Sequences dbmotifs STRING Filename of Motif Database inputs sequences dbmotifs neg upmotifs bfile Inputs scan_options local norc flip Scan Options threshold score optsc maxreg ethresh Thresholds output_options noseq Output Options @SERVICE_DIR@/centrimo_webservice false