Glimmer tutorial

1
Glimmer tutorial
2
Glimmer introduction

• A system for finding genes in microbial DNA,
  especially the genomes of bacteria and archaea.
  It uses interpolated Markov models (IMMs) to
  identify the coding regions and distinguish them
  from noncoding DNA
• Nucleic Acids Research paper on Glimmer 1.0
• Nucleic Acids Research, 1998, Vol. 26, P544548
  PMID9421513
• Subsequent paper on Glimmer 2.0
• Nucleic Acids Research, 1999, Vol. 27,
  P4636-4641PMID10556321
• http//cbcb.umd.edu/software/glimmer/

3
Glimmer 2 (quickstart)

• gtrun-glimmer2 genome
• 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.

4
Running glimmer 4 steps

• 1. long-orfs
• 2. extract
• 3. build-icm
• 4. glimmer2

5

• Long-orfs
• USAGE ./long-orfs ltgenome-filegt options
• Compute the optimal length for minimum "long
  orfs
• extract
• Usages extract genome_file coord_file
• 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.

6

• build-icm
• USAGE build-icm options
• Read sequences from standard input, build an
  Interpolated Context Model (ICM) for them, and
  output it to standard output

7

• glimmer2
• USAGE glimmer2 ltgenome-filegt lticm-filegt
  options
• Find/Score potential genes in ltgenome-filegt using
  the probability model in lticm-filegt
• get-putative
• This program extracts the list of putative genes
  from Glimmer output.

8
Homework

• Get unknown sequence (http//ym78123.ym.edu.tw/hom
  ework/unknown.fasta)
• Run gene prediction program (ex Glimmer)
• How many genes you can find?
• What are the functions of these genes?
• (optional) predict rRNA, tRNA, or other ncRNA