Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.

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Presentation transcript:

Glimmer and GeneMark

Glimmer Glimmer is a system for finding genes in microbial DNA 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 process 1.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 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