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TIGR-GLIMMER(1) 					      General Commands Manual						   TIGR-GLIMMER(1)

NAME
tigr-glimmer -- Fine start/stop positions of genes in genome sequence SYNOPSIS
tigr-extract [genome-file options] DESCRIPTION
Program extract takes a FASTA format sequence file and a file with a list of start/stop positions in that file (e.g., as produced by the long-orfs program) and extracts and outputs the specified sequences. The first command-line argument is the name of the sequence file, which must be in FASTA format. 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. The output of the program goes to the standard output and has one line for each line in the coordinate file. Each line contains the IDstring , followed by white space, followed by the substring of the sequence file specified by the coordinate pair. Specifically, the substring starts at the first position of the pair and ends at the second position (inclusive). If the first position is bigger than the second, then the DNA reverse complement of each position is generated. Start/stop pairs that "wrap around" the end of the genome are allowed. OPTIONS
-skip makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program. -l makes the output omit an sequences shorter than n characters. n includes the 3 skipped characters if the -skip switch is one. SEE ALSO
tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), tigr-check (1), tigr-codon-usage (1), tigr- compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1), http://www.tigr.org/software/glimmer/ Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR
This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system. TIGR-GLIMMER(1)

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Bio::Tools::Glimmer(3pm)				User Contributed Perl Documentation				  Bio::Tools::Glimmer(3pm)

NAME
Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions SYNOPSIS
use Bio::Tools::Glimmer; # file my $parser = Bio::Tools::Glimmer->new(-file => $file); # filehandle: $parser = Bio::Tools::Glimmer->new( -fh => *INPUT ); # provide a sequence identifier (Glimmer 2.X) my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname); # force format (override automatic detection) my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM'); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same while(my $gene = $parser->next_prediction()) { # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance # of Bio::Tools::Prediction::Gene, which inherits off # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an # array of Bio::Tools::Prediction::Exon objects. # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an # instance of Bio::SeqFeature::Generic # all exons (eukaryotic only): @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); } DESCRIPTION
This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse. Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>. GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>. GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>. Note that Glimmer 2.X will only process the first sequence in a fasta file, and the prediction report does not contain any sort of sequence identifier Note that Glimmer 3.X produces two output files. This module only parses the .predict file. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org CONTRIBUTORS
Torsten Seemann Mark Johnson APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Tools::Glimmer->new(); Function: Builds a new Bio::Tools::Glimmer object Returns : an instance of Bio::Tools::Glimmer Args : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname analysis_method Usage : $glimmer->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /glimmer/i. Returns : String Argument : n/a next_feature Title : next_feature Usage : while($gene = $glimmer->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : next_prediction Title : next_prediction Usage : while($gene = $glimmer->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : _parse_eukaryotic Title : _parse_eukaryotic() Usage : $obj->_parse_eukaryotic() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : _parse_prokaryotic Title : _parse_prokaryotic() Usage : $obj->_parse_prokaryotic() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE _seqname Title : _seqname Usage : $obj->_seqname($seqname) Function: internal (for Glimmer 2.X) Example : Returns : String _seqlength Title : _seqlength Usage : $obj->_seqlength($seqlength) Function: internal (for Glimmer 2.X) Example : Returns : String _format Title : _format Usage : $obj->_format($format) Function: internal Example : Returns : String _detail_file Title : _detail_file Usage : $obj->_detail_file($filename) Function: internal (for Glimmer 3.X) Example : Returns : String perl v5.14.2 2012-03-02 Bio::Tools::Glimmer(3pm)
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