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<HTML>
<HEAD>
<TITLE>
EMBOSS: cai
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
cai
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
CAI codon adaptation index
<H2>
Description
</H2>
<b>cai</b> calculates the <b>Codon Adaptation Index</b>. This is a
simple, effective measure of synonymous codon usage bias.
<p>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with cai</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>cai TEMBL:AB009602 </b>
CAI codon adaptation index
Codon usage file [Eyeast_cai.cut]: <b></b>
Output file [ab009602.cai]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-seqall]<br>(Parameter 1)</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-cfile</td>
<td>Codon usage table name</td>
<td>Codon usage file in EMBOSS data path</td>
<td>Eyeast_cai.cut</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.cai</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>cai</b> reads a nucleic acid sequence of a gene.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>Database entry: TEMBL:AB009602</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<b>cai</b> writes the Codon Adaptation Index to the output file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: ab009602.cai</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Sequence: AB009602 CAI: 0.188
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
<b>cai</b> reads a reference codon usage table prepared from a set of
genes which are known to be highly expressed.
<p>
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.
<p>
You should prepare your own codon usage table for your organism of interest.
<p>
<p>
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.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
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".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>
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.
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="chips.html">chips</a></td>
<td>Codon usage statistics</td>
</tr>
<tr>
<td><a href="codcmp.html">codcmp</a></td>
<td>Codon usage table comparison</td>
</tr>
<tr>
<td><a href="cusp.html">cusp</a></td>
<td>Create a codon usage table</td>
</tr>
<tr>
<td><a href="syco.html">syco</a></td>
<td>Synonymous codon usage Gribskov statistic plot</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (March 2001) - Alan Bleasby.
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
|
