
                                    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 CAI 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 sequence is calculated from the frequency of use of all codons in
   that gene sequence. 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

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

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -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
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated 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 standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -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
   

   Standard (Mandatory) qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -cfile Codon usage table name Codon usage file in EMBOSS data path
   Eyeastcai.cut
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.cai
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) 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="SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIA
E
FT                   RVSCPDQRFIFSTLEDVVEEYNKYESLPPGLLITGYSCNTLRNTA"
XX
SQ   Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
     gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt        6
0
     tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac       12
0
     cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg       18
0
     aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg       24
0
     gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt       30
0
     tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac       36
0
     ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt       42
0
     ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt       48
0
     tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa       54
0
     aacaattcta atggtcaaaa a                                                 56
1
//
   
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 © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   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
