| cai

## Function

CAI codon adaptation index

## Description

cai calculates the Codon Adaptation Index. This is a simple, effective measure of synonymous codon usage bias.

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.

## Usage

Here is a sample session with cai

    % cai TEMBL:AB009602
    CAI codon adaptation index
    Codon usage file [Eyeastcai.cut]:
    Output file [ab009602.cai]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Mandatory qualifiers:
      [-seqall]            seqall     Sequence database USA
       -cfile              codon      Codon usage file
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       Associated qualifiers:
      "-seqall" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related qualifiers
       -odirectory2         string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

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)

## Input file format

cai reads a nucleic acid sequence of a gene.

### Input files for usage example

### Database entry: TEMBL:AB009602

    ID   AB009602   standard; RNA; FUN; 561 BP.
    XX
    AC   AB009602;
    XX
    SV   AB009602.1
    XX
    DT   15-DEC-1997 (Rel. 53, Created)
    DT   15-DEC-1997 (Rel. 53, Last updated, Version 1)
    XX
    DE   Schizosaccharomyces pombe mRNA for MET1 homolog, partial cds.
    XX
    KW   MET1 homolog.
    XX
    OS   Schizosaccharomyces pombe (fission yeast)
    OC   Eukaryota; Fungi; Ascomycota; Schizosaccharomycetes;
    OC   Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces.
    XX
    RN   [1]
    RP   1-561
    RA   Kawamukai M.;
    RT   ;
    RL   Submitted (07-DEC-1997) to the EMBL/GenBank/DDBJ databases.
    RL   Makoto Kawamukai, Shimane University, Life and Environmental Science; 1060
    RL   Nishikawatsu, Matsue, Shimane 690, Japan
    RL   (E-mail:kawamuka@life.shimane-u.ac.jp, Tel:0852-32-6587, Fax:0852-32-6499)
    XX
    RN   [2]
    RP   1-561
    RA   Kawamukai M.;
    RT   "S.pmbe MET1 homolog";
    RL   Unpublished.
    XX
    DR   SPTREMBL; Q9URL1; Q9URL1.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..561
    FT                   /db_xref="taxon:4896"
    FT                   /sequenced_mol="cDNA to mRNA"
    FT                   /organism="Schizosaccharomyces pombe"
    FT                   /clone_lib="pGAD GH"
    FT   CDS             <1..275
    FT                   /codon_start=3
    FT                   /db_xref="SPTREMBL:Q9URL1"
    FT                   /transl_table=1
    FT                   /product="MET1 homolog"
    FT                   /protein_id="BAA23999.1"
    FT                   /translation="SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAE
    FT                   RVSCPDQRFIFSTLEDVVEEYNKYESLPPGLLITGYSCNTLRNTA"
    XX
    SQ   Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
         gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt        60
         tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac       120
         cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg       180
         aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg       240
         gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt       300
         tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac       360
         ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt       420
         ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt       480
         tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa       540
         aacaattcta atggtcaaaa a                                                 561
    //

## Output file format

cai writes the Codon Adaptation Index to the output file.

### Output files for usage example

### File: ab009602.cai

    Sequence: AB009602 CAI: 0.188

## Data files

cai reads a reference codon usage table prepared from a set of genes which are known to be highly expressed.

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:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

Sharp PM., Li W-H. "The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications." Nucleic Acids Research 1987 vol 15, pp 1281-1295.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

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

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

Written (March 2001) - Alan Bleasby.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments