]> scan a database with a sampled motif Neuwald, Lawrence gibbs_scan gibbs_scan perl "/local/gensoft/bin/scan " 0 motif_file Motif scan file (file.sn) perl " $value" 2 gibbs_motif perl 1 db Database perl " /local/gensoft/lib/gibbs/db/$value" nrprot &protdbs; &nucdbs; 1 control_options Control options 4 e_value Maximum E-value detected (-e) perl (defined $value)? " -e$value" : "" 4 p_value Minimum -log10(P-value) required for each motif (-E) perl (defined $value)? " -E$value" : "" 4 repeats Scan for repeats (-r) perl ($value)? " -r" : "" 0 4 max_repeats Maximum number of repeats per sequence (-M) perl (defined $value)? " -M$value" : "" 4 perl $repeats min_repeats Minimum number of repeats per sequence (-m) perl (defined $value)? " -m$value" : "" 4 perl $repeats order Require motifs to be in correct order (-o) perl ($value)? " -o" : "" 0 4 product Use product multinomial model instead of Gribskov method (-P) perl ($value)? " -P" : "" 0 4 pseudo_count Pseudo counts for product multinomial model (-p) perl (defined $value)? " -p$value" : "" 4 perl $product shuffle Shuffle input sequences (-S) perl ($value)? " -S" : "" 4 seed Seed for random number generator (-s) perl (defined $value)? " -s$value" : "" 4 mask Mask out sequence regions... perl ($value)? " $value" : "" 4 -X -X: ... NOT matching motif(s) -x -x: ... matching motif(s) heap Size of heap for saving sequences (-h) perl (defined $value)? " -h$value" : "" 4 output_options Output options 4 seqfile Create sequence file for output (-c) perl ($value)? " -c" : "" 0 4