2.0.2 long-orfs - computes positions of the long orfs in the sequence 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 long_orfs long_orfs perl "long-orfs" 0 genome_sequence Genome sequence file perl " $value" 1 8 circular circular genome (-l) perl ($value) ? "" : " -l" 1 2 If the genome is not circular, do not allow genes to 'wrap around' the end of the genome. gene_length minimum gene length (-g) perl (defined $value && $value != $vdef)? " -g $value ":"" 500 2 Minimum gene length is the length of the smallest fragment considered to be a gene. The length is measured from the first base of the start codon to the last base *before* the stop codon. This value can be specified when running the program with the -g option. overlap_length minimum overlap length (-o) perl (defined $value && $value != $vdef)? " -o $value ":"" 30 2 Minimum overlap length is a lower bound on the number of bases overlap between 2 genes that is considered a problem. Overlaps shorter than this are ignored. overlap_percent minimum overlap percent (-p) perl (defined $value && $value != $vdef)? " -p $value ":"" 10 2 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* genes are ignored. If you *DON'T* want to eliminate overlappinggenes, just use the -p 100 option. genome_sequence_as_out $genome_sequence 100 orfs_coord "long_orfs.out" 100 glimmer_orfs_list perl 1 glimmer_orfs_list genome_sequence_as_out=genome_sequence