2.0 Search for genes S. Salzberg A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER. Nucleic Acids Research, 27:23, 4636-4641. S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models. Nucleic Acids Research 26:2 (1998), 544-548. http://bioweb.pasteur.fr/docs/gensoft-na.html#GLIMMER glimmer glimmer perl glimmer 0 genome_sequence Genome sequence file perl " $value" 1 8 models Markov models for genes as produced by the program build-icm. perl " $value" 2 model perl 1 min_length minimum gene length (-g) perl (defined $value && $value != $vdef)? " -g $value " : "" 90 3 Minimum gene length is the length of the smallest fragmentconsidered to be a gene. The length is measured from the first base of the start codon to the last base *before* the stop codon. circular Regard genome as circular (-l) perl ($value) ? "" : " -l" 1 3 min_olap minimum overlap length (-o) perl (defined $value && $value != $vdef)? " -o $value " : "" 30 3 Minimum overlap length is a lower bound on the number of bases overlap between 2 genes that is considered a problem. Overlaps shorter that this are ignored. min_olap_percent minimum overlap percent (-p) perl (defined $value && $value != $vdef)? " -p $value " : "" 10 3 Minimum overlap percent is another lower bound on the number of bases overlap that is considered a problem. Overlaps shorter than this percentage of *both* strings are ignored. threshold threshold score for calling as gene (-t) perl (defined $value && $value != $vdef)? " -t $value " : "" 90 3 Threshold score is the minimum in-frame score for a fragment to be considered a potential gene. start_choice use first codon in orf as start codon (default, +f) or use ribosome-binding energy to choose start codon (-f) perl ($value) ? "" : " -f" 1 3 Use first start codon indicates whether the first possible start codon is used or not. If not, the function Choose_Start is called to choose the start codon. Currently it computes hybridization energy between the string Ribosome_Pattern and the region in front of the start codon, and if this is above a threshold, that start site is chosen. The ribosome pattern string can be set by the -s option. Presumably function Choose_Start should be modified to do something cleverer. Currently used start codons are atg, gtg & ttg . These can be changed in the function Is_Start , but corresponding changes should be made in Choose_Start . rbs Use this string as the ribosome binding pattern to find start codons. (-s) perl (defined $value && $value ne $vdef)? " -s $value" : "" tcctcca 15 3 Use first start codon indicates whether the first possible start codon is used or not. If not, the function Choose_Start is called to choose the start codon. Currently it computes hybridization energy between the string Ribosome_Pattern and the region in front of the start codon, and if this is above a threshold, that start site is chosen. The ribosome pattern string can be set by the -s option. Presumably function Choose_Start should be modified to do something cleverer. indep_scores Use independent probability score column (default, +r), or don't use it (-r) perl ($value)? "" : " -r " 1 3 Use independent scores indicates whether the last column that scores each fragment using independent base probabilities is present. weak Use 'weak' scores on potential genes at least n bases long (-w) perl (defined $value) ? " -w $value" : "" Weak scores ignore the independent model.