Glimmer is a system for finding genes in microbial DNA, especially the
genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
Markov Modeler) uses interpolated Markov models (IMMs) to identify the
coding regions and distinguish them from noncoding DNA. The IMM approach,
described in our Nucleic Acids Research paper on Glimmer 1.0, uses a
combination of Markov models from first through eighth order, weighting
each model according to its predictive power. Glimmer 1.0 and 2.0 use
3-periodic nonhomogenous Markov models in their IMMs. 

Glimmer is the primary gene finder at TIGR, and has been used to annotate
the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997),
T. pallidum (Fraser et al., Science, July 1998), T. maritima,
D. radiodurans, M. tuberculosis, and non-TIGR projects such as
C. trachomatis, C. pneumoniae, and others. Its analyses of some of these
genomes and others is available at the TIGR microbial database site. 

Inprovements in the new system are discribed in a forthcoming paper in
the Dec. 1, 1999 issue of Nucleic Acids Research.

Glimmer 2.0 is described in:
  A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
  Improved Microbial Gene Identification with Glimmer.  
  Nucleic Acids Research, 1999, in press.
Please reference this paper if you use the system as part of any
published research.  

Note that Glimmer 1.0 is described in
  S. Salzberg, A. Delcher, S. Kasif, and O. White.
  Microbial Gene Identification using Interpolated Markov Models.
  Nucleic Acids Research, 26:2 (1998), 544-548.

Quickstart: if you just want to run Glimmer 2.0 on your genome
and you don't want to adjust any parameters (although we don't
recommend this), you can simply run it with the included run-glimmer2
script.

socr:<x> run-glimmer2 mygenome

run-glimmer2 will create an Interpolated Markov Model of your genome
and store it in a binary file called tmp.model.  It will store
the predicted gene coordinates in g2.coord.  Along the way
it will extract long ORFs and store them and their coordinates
in tmp.train and tmp.coord.

Recommended: read the readmes.

Glimmer 1.0 had 4 readme files, and Glimmer 2.0 maintains that
structure.  The four main programs are:
  1. long-orfs
  2. glim-extract
  3. build-icm
  4. glimmer2

    This file and all files in this release of the Glimmer system are
    copyright (c) 1999 by Arthur Delcher, Steven Salzberg, Simon
    Kasif, and Owen White.  All rights reserved.  Redistribution
    is not permitted without the express written permission of
    the authors.

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