motif sampling Neuwald & Lawrence Neuwald, Liu, and Lawrence (1995). Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Science 4, 1618-1632. (for Gibbs site sampling, Gibbs motif sampling, purge, and scan programs) Lawrence, Altschul, Boguski, Liu, Neuwald and Wootton (1993) Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment, Science 262:208-214. (for Gibbs site sampling program) gibbs gibbs perl "gibbs " 0 sequence Sequences file perl ($purge)? " $sequence.b$score" : " $sequence" 1 8 lengths Lengths of elements for each type (eg: e1,e2) perl " $value" 2 format: long[,long] example: 18,18,18 expected Expected number of elements for each type (eg: l1,l2) (motif sampler) perl " $value" 3 format: long[,long] example: 18,18,18 purge Run purge to remove closely related sequences perl ($value)? "purge $sequence" : "" 0 -10 output_options Output options 4 scan Create a scan output file (file.sn) (-f) perl ($value)? " -f" : "" 0 4 control_options Control options 4 sites_options Sites sampler options 4 sites_cycles Maximum number of cycles in each run (-m) perl (defined $value)? " -m$value" : "" 4 element_order Use element order in probabilities (-o) perl ($value)? " -o" : "" 0 4 sites_pseudo_counts Pseudo counts for ordering model (-q) perl (defined $value)? " -q$value" : "" 4 readings Number of near-optimum readings taken (-R) perl (defined $value)? " -R$value" : "" 4 motif_options Motif sampler options 4 wilcoxon Output wilcoxon rank test information (-w) perl ($value)? " -w" : "" 0 4 fractional_weight Fractional weight (0 to 1.0) on priors (-W) perl (defined $value)? " -W$value" : "" 4 The value must be between 0 to 1.0 perl $value < 0 || $value > 1.0 cycles Number of cycles between shifts (sites sampler) or maximum number of cycles per run (motif sampler) (-c) perl (defined $value)? " -c$value" : "" 4 cutoff Prob. cutoff for near optimum sampling (-C) perl (defined $value)? " -C$value" : "" 4 (0 < Cutoff <= 1) perl $value < 0 || $value > 1 fragmentation Use fragmentation (-d) perl ($value)? "" : " -d" 1 4 convergence Rapid convergence limit (higher = longer to converge) (-L) perl (defined $value)? " -L$value" : "" 4 nucleic Use nucleic acid alphabet (-n) perl ($value)? " -n" : "" 0 4 pseudo_counts Number of pseudo counts for product multinomial model (-p) perl (defined $value)? " -p$value" : "" 4 shuffle Randomly shuffle input sequences (-r) perl ($value)? " -r" : "" 0 4 seed Seed for random number generator (-s) perl (defined $value)? " -s$value" : "" 4 sampling_runs Maximum number of sampling runs (-t) perl (defined $value)? " -t$value" : "" 4 low_complexity Remove protein low complexity regions (-x) perl ($value)? "" : " -x" 1 4 purge_options purge options perl $purge score Score threshold perl " $value" -9 perl $purge method Heuristic method perl ($value && $value ne $vdef)? " $value" : "" -b -8 -b -b: blast -e -e: exhaustive perl $purge keep Keep first sequence in the set (-q) perl ($value)? " -q" : "" 0 -8 perl $purge mask Use xnu to mask low complexity regions (-x) perl ($value)? "" : " -x" 1 -8 perl $purge purge_sep perl ";" -1 perl $purge purged_sequence perl $purge $sequence.b$score scan_file perl "" "$sequence.sn" gibbs_motif perl $scan