Glimmer and GeneMark

Glimmer

• Glimmer is a system for finding genes in microbial DNA

http://ccb.jhu.edu/software/glimmer/index.shtml

• The system works by creating a variable-length Markov model from a training set of genes and then using that model to attempt to identify all genes in a given DNA sequence.

Glimmer

• Local Installation on burrow.soic.indiana.edu:– /l/glimmer3.02/bin

• All the relevant code is in– /l/glimmer3.02/bin/

• I have added E.coli data in the following directory to play with:– /tmp/ecoli

Glimmer

• Running Glimmer involves a two-step process1. Building the model using known genes– /l/glimmer3.02/bin/build-icm -r run1.icm < /tmp/ecoli/ecoli-genes.fasta

2. Make gene predictions using glimmer3 program– /l/glimmer3.02/bin/glimmer3 -o50 -g110 -t30 /tmp/ecoli/ecoli.fna run1.icm

run1

• For more details please refer:– /l/glimmer3.02/glim302notes.pdf

GeneMark

• GeneMark includes a suite of software tools for predicting protein coding genes in various types of genomes

http://opal.biology.gatech.edu/

• The algorithms use Hidden Markov models reflecting the "grammar" of gene organization.

GeneMark

• Local Installation on burrow:– /l/gmsuite/

• You can run the code for prokaryotic gene prediction using the following command– /l/gmsuite/gmsn.pl --prok --format GFF /tmp/ecoli/ecoli.fna

• For more details please refer to:– /l/gmsuite/README.GeneMarkSuite