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cai |
The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.
% cai embl:AB009602 CAI codon adaptation index Codon usage file [Eyeastcai.cut]: Output file [ab009602.cai]:
Mandatory qualifiers: [-seqall] seqall Sequence database USA -cfile codon Codon usage file [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-seqall] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-cfile | Codon usage file | Codon usage file in EMBOSS data path | Eyeastcai.cut |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.cai |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
The output from the above example follows:
CAI = 0.188
The default codon usage table 'Eyeastcai.cut' was prepared from a set of S. pombe genes by Peter Rice.
You should prepare your own codon usage table for your organism of interest.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Program name | Description |
---|---|
chips | Codon usage statistics |
codcmp | Codon usage table comparison |
cusp | Create a codon usage table |
syco | Synonymous codon usage Gribskov statistic plot |