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  <TITLE>
  EMBOSS: backtranseq
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<table align=center border=0 cellspacing=0 cellpadding=0>
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<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>
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<b><font size="+6">
backtranseq
</font></b>
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</table>
<br>&nbsp;
<p>



<H2>
    Function
</H2>
Back translate a protein sequence
<H2>
    Description
</H2>


<b>backtranseq</b> takes a protein sequence and makes a best estimate of the
likely nucleic acid sequence it could have come from.  It does this by
using a codon frequency table. For each amino acid, the corresponding
most frequently occuring codon is used in the construction of the nucleic
acid sequence.

<h3>Codon usage table name</h3>

<b>backtranseq</b> reads in a data file containing the codon frequency
tables.  The default codon frequency table is 'Ehum.cut' - the human
codon frequency table.  It is important to use a codon frequency table
that is appropriate for the species that your protein comes from. 
See the <b>Data Files</b> section below for more details on these files.



<H2>
    Usage
</H2>
<b>Here is a sample session with backtranseq</b>
<p>
Note that this is a human protein and so the default human codon frequency file is used ie. is not specified 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>backtranseq </b>
Back translate a protein sequence
Input (gapped) protein sequence: <b>tsw:opsd_human</b>
(gapped) nucleotide output sequence [opsd_human.fasta]: <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>
<p>
<b>Example 2</b>
<p>
This uses a drosophila sequence and codon table. 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>backtranseq -cfile Edrome.cut </b>
Back translate a protein sequence
Input (gapped) protein sequence: <b>tsw:ach2_drome</b>
(gapped) nucleotide output sequence [ach2_drome.fasta]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.2">Go to the input files for this example</a><br><a href="#output.2">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:
  [-sequence]          sequence   (Gapped) protein sequence filename and
                                  optional format, or reference (input USA)
  [-outfile]           seqout     [<sequence>.<format>] (Gapped) nucleotide
                                  sequence filename and optional format
                                  (output USA)

   Additional (Optional) qualifiers:
   -cfile              codon      [Ehuman.cut] Codon usage table name

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

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       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>[-sequence]<br>(Parameter 1)</td>
<td>(Gapped) protein sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>(Gapped) nucleotide sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i>&lt;*&gt;</i>.<i>format</i></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>-cfile</td>
<td>Codon usage table name</td>
<td>Codon usage file in EMBOSS data path</td>
<td>Ehuman.cut</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>


Any DNA sequence USA.

<p>

<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:opsd_human</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   OPSD_HUMAN              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (Opsin-2).
GN   Name=RHO; Synonyms=OPN2;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84272729; PubMed=6589631;
RA   Nathans J., Hogness D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";
RL   Gene 167:317-320(1995).
RN   [6]
RP   REVIEW ON RP4 VARIANTS.
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;


<font color=red>  [Part of this file has been deleted for brevity]</font>

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -&gt; M (effect not known).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -&gt; P (in RP4).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -&gt; R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -&gt; K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -&gt; C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -&gt; R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -&gt; L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -&gt; R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -&gt; E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -&gt; E (in RP4).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -&gt; R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -&gt; M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -&gt; L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -&gt; M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -&gt; A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -&gt; L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -&gt; Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -&gt; R (in RP4).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -&gt; S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
</pre>
</td></tr></table><p>

<a name="input.2"></a>
<h3>Input files for usage example 2</h3>
<p><h3>Database entry: tsw:ach2_drome</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   ACH2_DROME              Reviewed;         576 AA.
AC   P17644; Q9VC73;
DT   01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1990, sequence version 1.
DT   03-APR-2007, entry version 78.
DE   Acetylcholine receptor subunit alpha-like 2 precursor.
GN   Name=nAcR-alpha-96Ab; Synonyms=Acr96Ab, AcrE, sad; ORFNames=CG6844;
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC   Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC   Ephydroidea; Drosophilidae; Drosophila.
OX   NCBI_TaxID=7227;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   TISSUE=Head;
RX   MEDLINE=90301489; PubMed=2114015; DOI=10.1093/nar/18.12.3640;
RA   Baumann A., Jonas P., Gundelfinger E.D.;
RT   "Sequence of D alpha 2, a novel alpha-like subunit of Drosophila
RT   nicotinic acetylcholine receptors.";
RL   Nucleic Acids Res. 18:3640-3640(1990).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   TISSUE=Head;
RX   MEDLINE=90353591; PubMed=2117557; DOI=10.1016/0014-5793(90)81170-S;
RA   Jonas P., Baumann A., Merz B., Gundelfinger E.D.;
RT   "Structure and developmental expression of the D alpha 2 gene encoding
RT   a novel nicotinic acetylcholine receptor protein of Drosophila
RT   melanogaster.";
RL   FEBS Lett. 269:264-268(1990).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   MEDLINE=90360975; PubMed=1697262;
RA   Sawruk E., Schloss P., Betz H., Schmitt B.;
RT   "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD, a
RT   novel developmentally regulated alpha-subunit.";
RL   EMBO J. 9:2671-2677(1990).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Berkeley;
RX   MEDLINE=20196006; PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA   Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA   Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA   George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA   Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
RA   Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
RA   Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
RA   Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
RA   Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
RA   Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
RA   Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,


<font color=red>  [Part of this file has been deleted for brevity]</font>

DR   IntAct; P17644; -.
DR   Ensembl; CG6844; Drosophila melanogaster.
DR   KEGG; dme:Dmel_CG6844; -.
DR   FlyBase; FBgn0000039; nAcR-alpha-96Ab.
DR   BioCyc; DMEL-XXX-02:DMEL-XXX-02-013190-MONOMER; -.
DR   BioCyc; DMEL-XXX-02:DMEL-XXX-02-013191-MONOMER; -.
DR   GermOnline; CG6844; Drosophila melanogaster.
DR   GO; GO:0005515; F:protein binding; IPI:IntAct.
DR   InterPro; IPR006029; Neu_channel_TM.
DR   InterPro; IPR006202; Neur_chan_lig_bd.
DR   InterPro; IPR006201; Neur_channel.
DR   InterPro; IPR002394; Nic_ach_rcpt.
DR   Gene3D; G3DSA:3.30.1100.20; Neur_chan_lig_bd; 1.
DR   PANTHER; PTHR18945; Neur_channel; 2.
DR   Pfam; PF02931; Neur_chan_LBD; 1.
DR   Pfam; PF02932; Neur_chan_memb; 1.
DR   PRINTS; PR00254; NICOTINICR.
DR   PRINTS; PR00252; NRIONCHANNEL.
DR   TIGRFAMs; TIGR00860; LIC; 1.
DR   PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
KW   Complete proteome; Glycoprotein; Ion transport; Ionic channel;
KW   Membrane; Postsynaptic membrane; Receptor; Signal; Transmembrane;
KW   Transport.
FT   SIGNAL        1     21       Probable.
FT   CHAIN        22    576       Acetylcholine receptor subunit alpha-like
FT                                2.
FT                                /FTId=PRO_0000000300.
FT   TOPO_DOM     22    261       Extracellular (Potential).
FT   TRANSMEM    262    285       Potential.
FT   TRANSMEM    293    311       Potential.
FT   TRANSMEM    327    346       Potential.
FT   TOPO_DOM    347    526       Cytoplasmic (Potential).
FT   TRANSMEM    527    545       Potential.
FT   CARBOHYD     65     65       N-linked (GlcNAc...) (Potential).
FT   CARBOHYD    254    254       N-linked (GlcNAc...) (Potential).
FT   CARBOHYD    570    570       N-linked (GlcNAc...) (Potential).
FT   DISULFID    169    183       By similarity.
FT   DISULFID    243    244       Associated with receptor activation (By
FT                                similarity).
SQ   SEQUENCE   576 AA;  65506 MW;  97D6A46CADC3F42F CRC64;
     MAPGCCTTRP RPIALLAHIW RHCKPLCLLL VLLLLCETVQ ANPDAKRLYD DLLSNYNRLI
     RPVSNNTDTV LVKLGLRLSQ LIDLNLKDQI LTTNVWLEHE WQDHKFKWDP SEYGGVTELY
     VPSEHIWLPD IVLYNNADGE YVVTTMTKAI LHYTGKVVWT PPAIFKSSCE IDVRYFPFDQ
     QTCFMKFGSW TYDGDQIDLK HISQKNDKDN KVEIGIDLRE YYPSVEWDIL GVPAERHEKY
     YPCCAEPYPD IFFNITLRRK TLFYTVNLII PCVGISYLSV LVFYLPADSG EKIALCISIL
     LSQTMFFLLI SEIIPSTSLA LPLLGKYLLF TMLLVGLSVV ITIIILNIHY RKPSTHKMRP
     WIRSFFIKRL PKLLLMRVPK DLLRDLAANK INYGLKFSKT KFGQALMDEM QMNSGGSSPD
     SLRRMQGRVG AGGCNGMHVT TATNRFSGLV GALGGGLSTL SGYNGLPSVL SGLDDSLSDV
     AARKKYPFEL EKAIHNVMFI QHHMQRQDEF NAEDQDWGFV AMVMDRLFLW LFMIASLVGT
     FVILGEAPSL YDDTKAIDVQ LSDVAKQIYN LTEKKN
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>


The output is a nucleotide sequence containing the most favoured back
translation of the specified protein, and using the specified
translation table (which defaults to human).

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: opsd_human.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;OPSD_HUMAN P08100 Rhodopsin (Opsin-2).
ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG
AGGAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG
GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC
GTGACCGTGCAGCACAAGAAGCTGAGGACCCCCCTGAACTACATCCTGCTGAACCTGGCC
GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC
GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC
GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGGTACGTGGTGGTGTGC
AAGCCCATGAGCAACTTCAGGTTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC
TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGGTACATCCCC
GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC
GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC
TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC
GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGGATGGTGATCATCATGGTGATCGCC
TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC
AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC
TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGGAACTGCATGCTGACCACC
ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC
GAGACCAGCCAGGTGGCCCCCGCC
</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: ach2_drome.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;ACH2_DROME P17644 Acetylcholine receptor subunit alpha-like 2 precursor.
ATGGCCCCCGGCTGCTGCACCACCCGCCCCCGCCCCATCGCCCTGCTGGCCCACATCTGG
CGCCACTGCAAGCCCCTGTGCCTGCTGCTGGTGCTGCTGCTGCTGTGCGAGACCGTGCAG
GCCAACCCCGATGCCAAGCGCCTGTACGATGATCTGCTGAGCAACTACAACCGCCTGATC
CGCCCCGTGAGCAACAACACCGATACCGTGCTGGTGAAGCTGGGCCTGCGCCTGAGCCAG
CTGATCGATCTGAACCTGAAGGATCAGATCCTGACCACCAACGTGTGGCTGGAGCACGAG
TGGCAGGATCACAAGTTCAAGTGGGATCCCAGCGAGTACGGCGGCGTGACCGAGCTGTAC
GTGCCCAGCGAGCACATCTGGCTGCCCGATATCGTGCTGTACAACAACGCCGATGGCGAG
TACGTGGTGACCACCATGACCAAGGCCATCCTGCACTACACCGGCAAGGTGGTGTGGACC
CCCCCCGCCATCTTCAAGAGCAGCTGCGAGATCGATGTGCGCTACTTCCCCTTCGATCAG
CAGACCTGCTTCATGAAGTTCGGCAGCTGGACCTACGATGGCGATCAGATCGATCTGAAG
CACATCAGCCAGAAGAACGATAAGGATAACAAGGTGGAGATCGGCATCGATCTGCGCGAG
TACTACCCCAGCGTGGAGTGGGATATCCTGGGCGTGCCCGCCGAGCGCCACGAGAAGTAC
TACCCCTGCTGCGCCGAGCCCTACCCCGATATCTTCTTCAACATCACCCTGCGCCGCAAG
ACCCTGTTCTACACCGTGAACCTGATCATCCCCTGCGTGGGCATCAGCTACCTGAGCGTG
CTGGTGTTCTACCTGCCCGCCGATAGCGGCGAGAAGATCGCCCTGTGCATCAGCATCCTG
CTGAGCCAGACCATGTTCTTCCTGCTGATCAGCGAGATCATCCCCAGCACCAGCCTGGCC
CTGCCCCTGCTGGGCAAGTACCTGCTGTTCACCATGCTGCTGGTGGGCCTGAGCGTGGTG
ATCACCATCATCATCCTGAACATCCACTACCGCAAGCCCAGCACCCACAAGATGCGCCCC
TGGATCCGCAGCTTCTTCATCAAGCGCCTGCCCAAGCTGCTGCTGATGCGCGTGCCCAAG
GATCTGCTGCGCGATCTGGCCGCCAACAAGATCAACTACGGCCTGAAGTTCAGCAAGACC
AAGTTCGGCCAGGCCCTGATGGATGAGATGCAGATGAACAGCGGCGGCAGCAGCCCCGAT
AGCCTGCGCCGCATGCAGGGCCGCGTGGGCGCCGGCGGCTGCAACGGCATGCACGTGACC
ACCGCCACCAACCGCTTCAGCGGCCTGGTGGGCGCCCTGGGCGGCGGCCTGAGCACCCTG
AGCGGCTACAACGGCCTGCCCAGCGTGCTGAGCGGCCTGGATGATAGCCTGAGCGATGTG
GCCGCCCGCAAGAAGTACCCCTTCGAGCTGGAGAAGGCCATCCACAACGTGATGTTCATC
CAGCACCACATGCAGCGCCAGGATGAGTTCAACGCCGAGGATCAGGATTGGGGCTTCGTG
GCCATGGTGATGGATCGCCTGTTCCTGTGGCTGTTCATGATCGCCAGCCTGGTGGGCACC
TTCGTGATCCTGGGCGAGGCCCCCAGCCTGTACGATGATACCAAGGCCATCGATGTGCAG
CTGAGCGATGTGGCCAAGCAGATCTACAACCTGACCGAGAAGAAGAAC
</pre>
</td></tr></table><p>


<H2>
    Data files
</H2>


The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS'
directory of the EMBOSS distribution.  If the name of a codon usage file
is specified on the command line, then this file will first be searched
for in the current directory and then in the 'data/CODONS' directory of
the EMBOSS distribution. 

<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>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>


"Corrupt codon index file" - the codon usage file is incomplete or empty.

<p>
"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.

<H2>
    Exit status
</H2>


This program always exits with a status of 0, unless the codon usage
table cannot be opened.

<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="backtranambig.html">backtranambig</a></td>
<td>Back translate a protein sequence to ambiguous codons</td>
</tr>

<tr>
<td><a href="charge.html">charge</a></td>
<td>Protein charge plot</td>
</tr>

<tr>
<td><a href="checktrans.html">checktrans</a></td>
<td>Reports STOP codons and ORF statistics of a protein</td>
</tr>

<tr>
<td><a href="coderet.html">coderet</a></td>
<td>Extract CDS, mRNA and translations from feature tables</td>
</tr>

<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Count composition of dimer/trimer/etc words in a sequence</td>
</tr>

<tr>
<td><a href="emowse.html">emowse</a></td>
<td>Protein identification by mass spectrometry</td>
</tr>

<tr>
<td><a href="freak.html">freak</a></td>
<td>Residue/base frequency table or plot</td>
</tr>

<tr>
<td><a href="iep.html">iep</a></td>
<td>Calculates the isoelectric point of a protein</td>
</tr>

<tr>
<td><a href="mwcontam.html">mwcontam</a></td>
<td>Shows molwts that match across a set of files</td>
</tr>

<tr>
<td><a href="mwfilter.html">mwfilter</a></td>
<td>Filter noisy molwts from mass spec output</td>
</tr>

<tr>
<td><a href="octanol.html">octanol</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepinfo.html">pepinfo</a></td>
<td>Plots simple amino acid properties in parallel</td>
</tr>

<tr>
<td><a href="pepstats.html">pepstats</a></td>
<td>Protein statistics</td>
</tr>

<tr>
<td><a href="pepwindow.html">pepwindow</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepwindowall.html">pepwindowall</a></td>
<td>Displays protein hydropathy of a set of sequences</td>
</tr>

<tr>
<td><a href="plotorf.html">plotorf</a></td>
<td>Plot potential open reading frames</td>
</tr>

<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>Output sequence with translated ranges</td>
</tr>

<tr>
<td><a href="remap.html">remap</a></td>
<td>Display sequence with restriction sites, translation etc</td>
</tr>

<tr>
<td><a href="showorf.html">showorf</a></td>
<td>Pretty output of DNA translations</td>
</tr>

<tr>
<td><a href="showseq.html">showseq</a></td>
<td>Display a sequence with features, translation etc</td>
</tr>

<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>

<tr>
<td><a href="transeq.html">transeq</a></td>
<td>Translate nucleic acid sequences</td>
</tr>

</table>
<H2>
    Author(s)
</H2>
Alan Bleasby (ajb&nbsp;&copy;&nbsp;ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK



<H2>
    History
</H2>


Completed 6 Oct 1999

<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


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