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cai |
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.
% cai TEMBL:AB009602 CAI codon adaptation index Codon usage file [Eyeast_cai.cut]: Output file [ab009602.cai]: |
Go to the input files for this example
Go to the output files for this example
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 messages
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-seqall] (Parameter 1) |
Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -cfile | Codon usage table name | Codon usage file in EMBOSS data path | Eyeast_cai.cut |
| [-outfile] (Parameter 2) |
Output file name | Output file | <*>.cai |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
ID AB009602; SV 1; linear; mRNA; STD; FUN; 561 BP.
XX
AC AB009602;
XX
DT 15-DEC-1997 (Rel. 53, Created)
DT 14-APR-2005 (Rel. 83, Last updated, Version 2)
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
FH Key Location/Qualifiers
FH
FT source 1..561
FT /organism="Schizosaccharomyces pombe"
FT /mol_type="mRNA"
FT /clone_lib="pGAD GH"
FT /db_xref="taxon:4896"
FT CDS <1..275
FT /codon_start=3
FT /transl_table=1
FT /product="MET1 homolog"
FT /db_xref="GENEDB:SPCC1739.06c"
FT /db_xref="GOA:O74468"
FT /db_xref="UniProtKB/Swiss-Prot:O74468"
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
//
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Sequence: AB009602 CAI: 0.188 |
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:
| 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 |