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<HEAD>
  <TITLE>
  EMBOSS: getorf
  </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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
getorf
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Find and extract open reading frames (ORFs)
<H2>
    Description
</H2>
<p>This program finds and outputs the sequences of open reading frames (ORFs) in one or more nucleotide sequences.  An ORF may be defined as a region of a specified minimum size between two STOP codons, or between a START and a STOP codon.  The ORFs can be output as the nucleotide sequence or as the protein translation. Optionally, the program will output the region around the START codon, the first STOP codon, or the final STOP codon of an ORF. The START and STOP codons are defined in a Genetic Code table; a suitable table can be selected for the organism you are investigating. The output is a sequence file containing predicted open reading frames longer than the minimum size, which defaults to 30 bases (i.e. 10 amino acids).</p>

<H2>
    Usage
</H2>
Here is a sample session with <b>getorf</b>
<p>

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

% <b>getorf -minsize 300 </b>
Find and extract open reading frames (ORFs)
Input nucleotide sequence(s): <b>tembl:v00294</b>
protein output sequence(s) [v00294.orf]: <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>
Find and extract open reading frames (ORFs)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [<sequence>.<format>] Protein sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers:
   -table              menu       [0] Code to use (Values: 0 (Standard); 1
                                  (Standard (with alternative initiation
                                  codons)); 2 (Vertebrate Mitochondrial); 3
                                  (Yeast Mitochondrial); 4 (Mold, Protozoan,
                                  Coelenterate Mitochondrial and
                                  Mycoplasma/Spiroplasma); 5 (Invertebrate
                                  Mitochondrial); 6 (Ciliate Macronuclear and
                                  Dasycladacean); 9 (Echinoderm
                                  Mitochondrial); 10 (Euplotid Nuclear); 11
                                  (Bacterial); 12 (Alternative Yeast Nuclear);
                                  13 (Ascidian Mitochondrial); 14 (Flatworm
                                  Mitochondrial); 15 (Blepharisma
                                  Macronuclear); 16 (Chlorophycean
                                  Mitochondrial); 21 (Trematode
                                  Mitochondrial); 22 (Scenedesmus obliquus);
                                  23 (Thraustochytrium Mitochondrial))
   -minsize            integer    [30] Minimum nucleotide size of ORF to
                                  report (Any integer value)
   -maxsize            integer    [1000000] Maximum nucleotide size of ORF to
                                  report (Any integer value)
   -find               menu       [0] This is a small menu of possible output
                                  options. The first four options are to
                                  select either the protein translation or the
                                  original nucleic acid sequence of the open
                                  reading frame. There are two possible
                                  definitions of an open reading frame: it can
                                  either be a region that is free of STOP
                                  codons or a region that begins with a START
                                  codon and ends with a STOP codon. The last
                                  three options are probably only of interest
                                  to people who wish to investigate the
                                  statistical properties of the regions around
                                  potential START or STOP codons. The last
                                  option assumes that ORF lengths are
                                  calculated between two STOP codons. (Values:
                                  0 (Translation of regions between STOP
                                  codons); 1 (Translation of regions between
                                  START and STOP codons); 2 (Nucleic sequences
                                  between STOP codons); 3 (Nucleic sequences
                                  between START and STOP codons); 4
                                  (Nucleotides flanking START codons); 5
                                  (Nucleotides flanking initial STOP codons);
                                  6 (Nucleotides flanking ending STOP codons))

   Advanced (Unprompted) qualifiers:
   -[no]methionine     boolean    [Y] START codons at the beginning of protein
                                  products will usually code for Methionine,
                                  despite what the codon will code for when it
                                  is internal to a protein. This qualifier
                                  sets all such START codons to code for
                                  Methionine by default.
   -circular           boolean    [N] Is the sequence circular
   -[no]reverse        boolean    [Y] Set this to be false if you do not wish
                                  to find ORFs in the reverse complement of
                                  the sequence.
   -flanking           integer    [100] If you have chosen one of the options
                                  of the type of sequence to find that gives
                                  the flanking sequence around a STOP or START
                                  codon, this allows you to set the number of
                                  nucleotides either side of that codon to
                                  output. If the region of flanking
                                  nucleotides crosses the start or end of the
                                  sequence, no output is given for this codon.
                                  (Any integer value)

   Associated qualifiers:

   "-sequence" 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" 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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqall</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 bgcolor="#FFFFCC">
<td>[-outseq]<br>(Parameter 2)</td>
<td>seqoutall</td>
<td>Protein sequence set(s) filename and optional format (output USA)</td>
<td>Writeable sequence(s)</td>
<td><i>&lt;*&gt;</i>.<i>format</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-table</td>
<td>list</td>
<td>Code to use</td>
<td><table><tr><td>0</td> <td><i>(Standard)</i></td></tr><tr><td>1</td> <td><i>(Standard (with alternative initiation codons))</i></td></tr><tr><td>2</td> <td><i>(Vertebrate Mitochondrial)</i></td></tr><tr><td>3</td> <td><i>(Yeast Mitochondrial)</i></td></tr><tr><td>4</td> <td><i>(Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)</i></td></tr><tr><td>5</td> <td><i>(Invertebrate Mitochondrial)</i></td></tr><tr><td>6</td> <td><i>(Ciliate Macronuclear and Dasycladacean)</i></td></tr><tr><td>9</td> <td><i>(Echinoderm Mitochondrial)</i></td></tr><tr><td>10</td> <td><i>(Euplotid Nuclear)</i></td></tr><tr><td>11</td> <td><i>(Bacterial)</i></td></tr><tr><td>12</td> <td><i>(Alternative Yeast Nuclear)</i></td></tr><tr><td>13</td> <td><i>(Ascidian Mitochondrial)</i></td></tr><tr><td>14</td> <td><i>(Flatworm Mitochondrial)</i></td></tr><tr><td>15</td> <td><i>(Blepharisma Macronuclear)</i></td></tr><tr><td>16</td> <td><i>(Chlorophycean Mitochondrial)</i></td></tr><tr><td>21</td> <td><i>(Trematode Mitochondrial)</i></td></tr><tr><td>22</td> <td><i>(Scenedesmus obliquus)</i></td></tr><tr><td>23</td> <td><i>(Thraustochytrium Mitochondrial)</i></td></tr></table></td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-minsize</td>
<td>integer</td>
<td>Minimum nucleotide size of ORF to report</td>
<td>Any integer value</td>
<td>30</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-maxsize</td>
<td>integer</td>
<td>Maximum nucleotide size of ORF to report</td>
<td>Any integer value</td>
<td>1000000</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-find</td>
<td>list</td>
<td>This is a small menu of possible output options. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons. The last option assumes that ORF lengths are calculated between two STOP codons.</td>
<td><table><tr><td>0</td> <td><i>(Translation of regions between STOP codons)</i></td></tr><tr><td>1</td> <td><i>(Translation of regions between START and STOP codons)</i></td></tr><tr><td>2</td> <td><i>(Nucleic sequences between STOP codons)</i></td></tr><tr><td>3</td> <td><i>(Nucleic sequences between START and STOP codons)</i></td></tr><tr><td>4</td> <td><i>(Nucleotides flanking START codons)</i></td></tr><tr><td>5</td> <td><i>(Nucleotides flanking initial STOP codons)</i></td></tr><tr><td>6</td> <td><i>(Nucleotides flanking ending STOP codons)</i></td></tr></table></td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]methionine</td>
<td>boolean</td>
<td>START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein. This qualifier sets all such START codons to code for Methionine by default.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-circular</td>
<td>boolean</td>
<td>Is the sequence circular</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]reverse</td>
<td>boolean</td>
<td>Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-flanking</td>
<td>integer</td>
<td>If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon.</td>
<td>Any integer value</td>
<td>100</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outseq" associated seqoutall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osformat2<br>-osformat_outseq</td>
<td>string</td>
<td>Output seq format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osextension2<br>-osextension_outseq</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osname2<br>-osname_outseq</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osdirectory2<br>-osdirectory_outseq</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osdbname2<br>-osdbname_outseq</td>
<td>string</td>
<td>Database name to add</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ossingle2<br>-ossingle_outseq</td>
<td>boolean</td>
<td>Separate file for each entry</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -oufo2<br>-oufo_outseq</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -offormat2<br>-offormat_outseq</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofname2<br>-ofname_outseq</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofdirectory2<br>-ofdirectory_outseq</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<H2>
    Input file format
</H2>


<b>getorf</b> reads one or more nucleotide sequences.

<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>

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

'tembl:v00294' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:v00294</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   V00294; SV 1; linear; genomic DNA; STD; PRO; 1113 BP.
XX
AC   V00294;
XX
DT   09-JUN-1982 (Rel. 01, Created)
DT   10-FEB-1999 (Rel. 58, Last updated, Version 2)
XX
DE   E. coli laci gene (codes for the lac repressor).
XX
KW   DNA binding protein; repressor.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1-1113
RX   DOI; 10.1038/274765a0.
RX   PUBMED; 355891.
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene";
RL   Nature 274(5673):765-769(1978).
XX
CC   KST ECO.LACI
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1113
FT                   /organism="Escherichia coli"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:562"
FT   CDS             31..1113
FT                   /transl_table=11
FT                   /note="reading frame"
FT                   /db_xref="GOA:P03023"
FT                   /db_xref="InterPro:IPR000843"
FT                   /db_xref="InterPro:IPR010982"
FT                   /db_xref="PDB:1CJG"
FT                   /db_xref="PDB:1EFA"
FT                   /db_xref="PDB:1JWL"
FT                   /db_xref="PDB:1JYE"
FT                   /db_xref="PDB:1JYF"
FT                   /db_xref="PDB:1L1M"
FT                   /db_xref="PDB:1LBG"
FT                   /db_xref="PDB:1LBH"
FT                   /db_xref="PDB:1LBI"
FT                   /db_xref="PDB:1LCC"
FT                   /db_xref="PDB:1LCD"
FT                   /db_xref="PDB:1LQC"
FT                   /db_xref="PDB:1LTP"
FT                   /db_xref="PDB:1OSL"
FT                   /db_xref="PDB:1TLF"
FT                   /db_xref="PDB:1Z04"
FT                   /db_xref="PDB:2BJC"
FT                   /db_xref="PDB:2KEI"
FT                   /db_xref="PDB:2KEJ"
FT                   /db_xref="PDB:2KEK"
FT                   /db_xref="PDB:2P9H"
FT                   /db_xref="PDB:2PAF"
FT                   /db_xref="PDB:2PE5"
FT                   /db_xref="PDB:3EDC"
FT                   /db_xref="UniProtKB/Swiss-Prot:P03023"
FT                   /protein_id="CAA23569.1"
FT                   /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
FT                   NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
FT                   EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
FT                   EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
FT                   MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
FT                   YIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
FT                   ALADSLMQLARQVSRLESGQ"
XX
SQ   Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
     ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca        60
     gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt       120
     tctgcgaaaa cgcgggaaaa agtggaagcg gcgatggcgg agctgaatta cattcccaac       180
     cgcgtggcac aacaactggc gggcaaacag tcgttgctga ttggcgttgc cacctccagt       240
     ctggccctgc acgcgccgtc gcaaattgtc gcggcgatta aatctcgcgc cgatcaactg       300
     ggtgccagcg tggtggtgtc gatggtagaa cgaagcggcg tcgaagcctg taaagcggcg       360
     gtgcacaatc ttctcgcgca acgcgtcagt gggctgatca ttaactatcc gctggatgac       420
     caggatgcca ttgctgtgga agctgcctgc actaatgttc cggcgttatt tcttgatgtc       480
     tctgaccaga cacccatcaa cagtattatt ttctcccatg aagacggtac gcgactgggc       540
     gtggagcatc tggtcgcatt gggtcaccag caaatcgcgc tgttagcggg cccattaagt       600
     tctgtctcgg cgcgtctgcg tctggctggc tggcataaat atctcactcg caatcaaatt       660
     cagccgatag cggaacggga aggcgactgg agtgccatgt ccggttttca acaaaccatg       720
     caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg       780
     ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta       840
     gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa       900
     caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc       960
     caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg      1020
     gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca      1080
     cgacaggttt cccgactgga aagcgggcag tga                                   1113
//
</pre>
</td></tr></table><p>


<H2>
    Output file format
</H2>

<p>

The input is a standard EMBOSS sequence query (also known as a 'USA')
with associated feature information.

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the command-line qualifier
<tt>-sformat xxx</tt>, where 'xxx' is replaced by the name of the
required format.  The available format names are: text, html, xml (uniprotxml),
obo, embl (swissprot)

<p> Where the sequence format has no feature information, a second
file can be read to load the feature data. The file is specified with
the qualifier <tt>-ufo xxx</tt> and the feature format is specified with
the qualifier <tt>-fformat xxx</tt>

<p>
See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>
See:
<A href="http://emboss.sf.net/docs/themes/FeatureFormats.html">
http://emboss.sf.net/docs/themes/FeatureFormats.html</A>
for further information on feature formats.

<p>
The output is a sequence file containing predicted open reading frames
longer than the minimum size, which defaults to 30 bases (i.e. 10 amino acids).

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: v00294.orf</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;V00294_1 [735 - 1112] E. coli laci gene (codes for the lac repressor).
GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSP
AGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFP
TGKRAV
&gt;V00294_2 [1 - 1110] E. coli laci gene (codes for the lac repressor).
PEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN
RVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAA
VHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLG
VEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTM
QMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIK
QDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLA
RQVSRLESGQ
&gt;V00294_3 [465 - 49] (REVERSE SENSE) E. coli laci gene (codes for the lac repressor).
RRNISAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGA
RFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGL
VHHAGNGLIRDTGILCDIV
</pre>
</td></tr></table><p>

<p> 

The name of the ORF sequences is constructed from the name of the
input sequence with an underscore character ('_') and a unique ordinal number
of the ORF found appended.  The description of the output ORF sequence
is constructed from the description of the input sequence with the start
and end positions of the ORF prepended.  

<p>

The unique number appended to the name is simply used to create new
unique sequence names, it does not imply any further information
indicating any order, positioning or sense-strand of the ORFs. 

<p>

If the ORF has been found in the reverse sense, then the start position
will be smaller than the end position.  The numbering uses the
forward-sense positions, but read in the reverse sense.  For example,
<b>&gt;V00294_3 [465 - 49]</b> in the output above is a reverse-sense
ORF running from position 465 to 49.  The description will also contain
'(REVERSE SENSE)'. 

<p>

If the sequence has been specified as a circular genome (using the
command-line switch '-circular'), then ORFs can potentially continue
past the 'end' of the input sequence (the breakpoint of the circular
genome) and into the 'start' of the sequence again.  This is dealt with
by appending the sequence to itself three times and reporting long ORFs
that are found in this extended sequence.  Any ORF that is longer that
three times the sequence length (i.e one that continues without hitting
a STOP at any point in the genome) will be reported as being a maximum
of three times the length of the input sequence.  Note that the end
position of an ORF in circular genomes can be apparently longer than the
input sequence if the ORF crosses the breakpoint.  If the ORF crosses
the breakpoint, then the text '(ORF crosses the breakpoint)' will be
added to the description of the output sequence. 

<H2>
    Data files
</H2>

The START and STOP codons used by <b>getorf</b> are defined in the
Genetic Code data files. By default, Genetic Code file <b>EGC.0</b>
is used.
<p>

The default file <b>EGC.0</b> is the 'Standard Code' with the rarely
used alternate START codons omitted, it only has the normal 'AUG' START
codon.  The 'Standard Code' with the rarely used alternate START codons
included is Genetic Code file <b>EGC.1</b>. 

<p>

It is expected that user will sometimes wish to customise a Genetic Code
file. To do this, use the program <b>embossdata</b>.

<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>

<p>
The Genetic Code data files are based on the NCBI genetic code tables.
Their names and descriptions are:

<dl>
<dt>EGC.0 </dt><dd>
      Standard (Differs from GC.1 in that it only has initiation site 'AUG')
<dt>EGC.1 </dt><dd>
      Standard
<dt>EGC.2 </dt><dd>
      Vertebrate Mitochodrial
<dt>EGC.3 </dt><dd>
      Yeast Mitochondrial
<dt>EGC.4 </dt><dd>
      Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
<dt>EGC.5 </dt><dd>
      Invertebrate Mitochondrial
<dt>EGC.6 </dt><dd>
      Ciliate Macronuclear and Dasycladacean
<dt>EGC.9 </dt><dd>
      Echinoderm Mitochondrial
<dt>EGC.10 </dt><dd>
      Euplotid Nuclear
<dt>EGC.11 </dt><dd>
      Bacterial
<dt>EGC.12 </dt><dd>
      Alternative Yeast Nuclear
<dt>EGC.13 </dt><dd>
      Ascidian Mitochondrial
<dt>EGC.14 </dt><dd>
      Flatworm Mitochondrial
<dt>EGC.15</dt><dd>
      Blepharisma Macronuclear
<dt>EGC.16</dt><dd>
      Chlorophycean Mitochondrial
<dt>EGC.21</dt><dd>
      Trematode Mitochondrial
<dt>EGC.22</dt><dd>
      Scenedesmus obliquus
<dt>EGC.23</dt><dd>
      Thraustochytrium Mitochondrial
</dl>

<p>

The format of these files is very simple.

<p>   

It consists of several lines of optional comments, each starting with
a '#' character.

<p>

These are followed the line: 'Genetic Code [n]', where 'n' is the
number of the genetic code file.

<p> 

This is followed by the description of the code and then by four lines
giving the IUPAC one-letter code of the translated amino acid, the
start codons (indicdated by an 'M') and the three bases of the codon,
lined up one on top of the other.
   
<p>

For example:

<pre>
   
------------------------------------------------------------------------------
# Genetic Code Table
#
# Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
# and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
#
# Differs from Genetic Code [1] only in that the initiation sites have been
# changed to only 'AUG'

Genetic Code [0]
Standard
   
AAs  =   FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
------------------------------------------------------------------------------

</pre>



<H2>
    Notes
</H2>

<p>There are two common definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon.</p>

<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>


It always exits with status 0. 

<H2>
    Known bugs
</H2>

'-sbegin' and -send' do not work with this program.

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

<tr>
<td><a href="marscan.html">marscan</a></td>
<td>Find matrix/scaffold recognition (MRS) signatures in DNA sequences</td>
</tr>

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

<tr>
<td><a href="showorf.html">showorf</a></td>
<td>Display a nucleotide sequence and translation in pretty format</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="syco.html">syco</a></td>
<td>Draw synonymous codon usage statistic plot for a nucleotide sequence</td>
</tr>

<tr>
<td><a href="tcode.html">tcode</a></td>
<td>Identify protein-coding regions using Fickett TESTCODE statistic</td>
</tr>

<tr>
<td><a href="wobble.html">wobble</a></td>
<td>Plot third base position variability in a nucleotide sequence</td>
</tr>

</table>
<P>
<ul>

<li><a href="checktrans.html">checktrans</a> - Reports STOP codons
and ORF statistics of a protein sequence

</ul>

<H2>
    Author(s)
</H2>

Gary Williams formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>

2000 - written - Gary Williams

<p>

November 2002 - added indication of reverse sense ORFs

<p>

November 2002 - added indication of ORFs that cross the breakpoint at
position 1 in circular genomes. 

<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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