USAGE: glimmer3 [options] <sequence-file> <icm-file> <tag> Read DNA sequences in <sequence-file> and predict genes in them using the Interpolated Context Model in <icm-file>. Output details go to file <tag>.detail and predictions go to file <tag>.predict Options: -A <codon-list> --start_codons <codon-list> Use comma-separated list of codons as start codons Sample format: -A atg,gtg Use -P option to specify relative proportions of use. If -P not used, then proportions will be equal -b <filename> --rbs_pwm <filename> Read a position weight matrix (PWM) from <filename> to identify the ribosome binding site to help choose start sites -C <p> --gc_percent <p> Use <p> as GC percentage of independent model Note: <p> should be a percentage, e.g., -C 45.2 -E <filename> --entropy <filename> Read entropy profiles from <filename>. Format is one header line, then 20 lines of 3 columns each. Columns are amino acid, positive entropy, negative entropy. Rows must be in order by amino acid code letter -f --first_codon Use first codon in orf as start codon -g <n> --gene_len <n> Set minimum gene length to <n> -h --help Print this message -i <filename> --ignore <filename> <filename> specifies regions of bases that are off limits, so that no bases within that area will be examined -l --linear Assume linear rather than circular genome, i.e., no wraparound -L <filename> --orf_coords <filename> Use <filename> to specify a list of orfs that should be scored separately, with no overlap rules -M --separate_genes <sequence-file> is a multifasta file of separate genes to be scored separately, with no overlap rules -o <n> --max_olap <n> Set maximum overlap length to <n>. Overlaps this short or shorter are ignored. -P <number-list> --start_probs <number-list> Specify probability of different start codons (same number & order as in -A option). If no -A option, then 3 values for atg, gtg and ttg in that order. Sample format: -P 0.6,0.35,0.05 If -A is specified without -P, then starts are equally likely. -q <n> --ignore_score_len <n> Do not use the initial score filter on any gene <n> or more base long -r --no_indep Don't use independent probability score column -t <n> --threshold <n> Set threshold score for calling as gene to n. If the in-frame score >= <n>, then the region is given a number and considered a potential gene. -X --extend Allow orfs extending off ends of sequence to be scored -z <n> --trans_table <n> Use Genbank translation table number <n> for stop codons -Z <codon-list> --stop_codons <codon-list> Use comma-separated list of codons as stop codons Sample format: -Z tag,tga,taa