Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system...
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Transcript of Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system...
![Page 1: Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.](https://reader038.fdocuments.in/reader038/viewer/2022100501/56649d365503460f94a0dc76/html5/thumbnails/1.jpg)
Glimmer and GeneMark
![Page 2: Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.](https://reader038.fdocuments.in/reader038/viewer/2022100501/56649d365503460f94a0dc76/html5/thumbnails/2.jpg)
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.
![Page 3: Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.](https://reader038.fdocuments.in/reader038/viewer/2022100501/56649d365503460f94a0dc76/html5/thumbnails/3.jpg)
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
![Page 4: Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.](https://reader038.fdocuments.in/reader038/viewer/2022100501/56649d365503460f94a0dc76/html5/thumbnails/4.jpg)
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
![Page 5: Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.](https://reader038.fdocuments.in/reader038/viewer/2022100501/56649d365503460f94a0dc76/html5/thumbnails/5.jpg)
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.
![Page 6: Glimmer and GeneMark. Glimmer Glimmer is a system for finding genes in microbial DNA The system works.](https://reader038.fdocuments.in/reader038/viewer/2022100501/56649d365503460f94a0dc76/html5/thumbnails/6.jpg)
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