cai Function   CAI codon adaptation indexDescription   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 indexCodon usage file [Eyeast_cai.cut]: Output file [ab009602.cai]:    Go to the input files for this example   Go to the output files for this exampleCommand line arguments   Standard (Mandatory) qualifiers:  [-seqall]            seqall     Nucleotide sequence(s) filename and optional                                  format, or reference (input USA)   -cfile              codon      [Eyeast_cai.cut] Codon usage table name  [-outfile]           outfile    [*.cai] 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   "-cfile" associated qualifiers   -format             string     Data format   "-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 dying program messagesInput file format   cai reads a nucleic acid sequence of a gene.  Input files for usage example  Database entry: TEMBL:AB009602ID   AB009602   standard; RNA; FUN; 561 BP.XXAC   AB009602;XXSV   AB009602.1XXDT   15-DEC-1997 (Rel. 53, Created)DT   15-DEC-1997 (Rel. 53, Last updated, Version 1)XXDE   Schizosaccharomyces pombe mRNA for MET1 homolog, partial cds.XXKW   MET1 homolog.XXOS   Schizosaccharomyces pombe (fission yeast)OC   Eukaryota; Fungi; Ascomycota; Schizosaccharomycetes;OC   Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces.XXRN   [1]RP   1-561RA   Kawamukai M.;RT   ;RL   Submitted (07-DEC-1997) to the EMBL/GenBank/DDBJ databases.RL   Makoto Kawamukai, Shimane University, Life and Environmental Science; 1060RL   Nishikawatsu, Matsue, Shimane 690, JapanRL   (E-mail:kawamuka@life.shimane-u.ac.jp, Tel:0852-32-6587, Fax:0852-32-6499)XXRN   [2]RP   1-561RA   Kawamukai M.;RT   "S.pmbe MET1 homolog";RL   Unpublished.XXDR   SPTREMBL; Q9URL1; Q9URL1.XXFH   Key             Location/QualifiersFHFT   source          1..561FT                   /db_xref="taxon:4896"FT                   /sequenced_mol="cDNA to mRNA"FT                   /organism="Schizosaccharomyces pombe"FT                   /clone_lib="pGAD GH"FT   CDS             <1..275FT                   /codon_start=3FT                   /db_xref="SPTREMBL:Q9URL1"FT                   /transl_table=1FT                   /product="MET1 homolog"FT                   /protein_id="BAA23999.1"FT                   /translation="SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAEFT                   RVSCPDQRFIFSTLEDVVEEYNKYESLPPGLLITGYSCNTLRNTA"XXSQ   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: 0.188Data 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' is the standard set of   Saccharomyces cerevisiae highly expressed gene codon frequiencies.   Another table Eschpo_cai.cut was prepared from a set of   Schizosaccharomyces pombe genes by Peter Rice for the S. pombe   sequencing team at the Sanger Centre.   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)     * ~/.embossdataNotes   None.References    1. 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 plotAuthor(s)   Alan Bleasby (ajb