COUSIN (COdon Usage Similarity INdex)
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Basic calculation step
Pattern Analysis
Optimization Analysis
Simulation Analysis
Clustering Analysis
Create a Codon Usage Table
Compare two datasets
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Development
* Theses parameters are mandatory
FASTA sequences *
Codon Usage Table (
kazusa
format) *
Genetic Code *
1 - The Standard Code
2 - The Vertebrate Mitochondrial Code
3 - The Yeast Mitochondrial Code
4 - The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
5 - The Invertebrate Mitochondrial Code
6 - The Ciliate, Dasycladacean and Hexamita Nuclear Code
9 - The Echinoderm Mitochondrial Code
10 - The Euplotid Nuclear Code
11 - The Bacterial, Archaeal and Plant Plastid Code
12 - The Alternative Yeast Nuclear Code
13 - The Ascidian Mitochondrial Code
14 - The Flatworm Mitochondrial Code
15 - Blepharisma Nuclear Code
16 - Chlorophycean Mitochondrial Code
21 - Trematode Mitochondrial Code
22 - Scenedesmus obliquus Mitochondrial Code
23 - Thraustochytrium Mitochondrial Code
24 - Pterobranchia Mitochondrial Code
25 - Candidate Division SR1 and Gracilibacteria Code
26 - Pachysolen tannophilus Nuclear Code
27 - Karyorelict Nuclear Code
28 - Condylostoma Nuclear Code
29 - Mesodinium Nuclear Code
30 - Peritrich Nuclear Code
31 - Blastocrithidia Nuclear Code
33 - Cephalodiscidae Mitochondrial UAA-Tyr Code
Example
Optimal codons (FOP, CBI methods)
Genetic Code *
DNA
AA (amino acids)
Optimization type *
1 - Random
2 - Random Guided
3 - Random with max GC content
4 - Random Guided with max GC content
5 - Random with max AT content
6 - Random Guided with max AT content
7 - One amino acid - One codon (Codons with highest frequencies)
8 - One amino acid - One codon (Codons with lowest frequencies)
Number of optimizations
10
Reverse frequencies
0 - Don't
1 - Do
Perform basic simulation ?
Remove COUSIN boundaries (default -3;4)
Create vectors for each query ?
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Do the analysis
