2.0.2 glimmer_extract - extracts subsequences corresponding to long orfs 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_extract glimmer_extract perl "glimmer-extract" 0 genome_sequence Genome sequence file perl " $value" 1 8 list_coord list of start/stop pairs perl " $value" 2 The second command-line argument is the name of the coordinate file. It must contain a list of pairs of positions in the first file, one per line. The format of each entry is: 'IDstring' 'start position' 'stop position' This file should contain no other information, so if you're using the output of glimmer or long-orfs , you'll have to cut off header lines. glimmer_orfs_list perl 1 glimmer_orfs_list genome_sequence skip skip the start codon (-skip) perl ($value)? " -skip" : "" 3 makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the default behaviour of the previous version of the program. min_length minimum length of sequences (-l) perl ($value)? " -l $value" : "" 3 makes the output omit any sequences shorter than n characters. n includes the 3 skipped characters if the -skip switch is on. outfile perl "" "glimmer_extract.out" 100 orfs perl 1