EMBOSS: getorf

| ## EMBOSS: getorf

# Program getorf

## Function

Finds and extracts open reading frames (ORFs)

## Description

This program finds and outputs the sequences of open reading frames (ORFs).

The ORFs can be defined as regions of a specified minimum size between STOP codons or between START and STOP codons.

The ORFs can be output as the nucleotide sequence or as the translation.

The program can also output the region around the START or the initial STOP codon or the ending STOP codons of an ORF for those doing analysis of the properties of these regions.

The START and STOP codons are defined in the Genetic Code tables. A suitable Genetic Code table can be selected for the organism you are investigating.

## Usage

Here is a sample session with getorf.

    % getorf -minsize 300
    Input sequence: embl:eclaci
    Output sequence [eclaci.orf]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers:
       -table              menu       Code to use
       -minsize            integer    Minimum nucleotide size of ORF to report
       -find               menu       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.

       Advanced qualifiers:
       -[no]methionine     bool       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           bool       Is the sequence circular
       -[no]reverse        bool       Set this to be false if you do not wish to
                                      find ORFs in the reverse complement of the
                                      sequence.
       -flanking           integer    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.

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
-table | Code to use |
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)
| 0
-minsize | Minimum nucleotide size of ORF to report | Any integer value | 30
-find | 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. |
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)
| 0
Advanced qualifiers | Allowed values | Default
-[no]methionine | 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. | Yes/No | Yes
-circular | Is the sequence circular | Yes/No | No
-[no]reverse | Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence. | Yes/No | Yes
-flanking | 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 | 100

## Input file format

Any nucleic acid sequence USA.

## Output file format

The output is a sequence file containing predicted open reading frames longer than the minimum size, which defaults to 30 bases or 10 amino acids.

The results from the example run are:

    >ECLACI_1 [735 - 1112] E. coli laci gene (codes for the lac repressor).
    GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSP
    AGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFP
    TGKRAV
    >ECLACI_2 [1 - 1110] E. coli laci gene (codes for the lac repressor).
    PEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN
    RVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAA
    VHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLG
    VEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTM
    QMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIK
    QDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLA
    RQVSRLESGQ*
    >ECLACI_3 [465 - 49] E. coli laci gene (codes for the lac repressor).
    RRNISAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGA
    RFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGL
    VHHAGNGLIRDTGILCDIV

All output ORF sequences are written to the specified outut file.

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.

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.

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, >ECLACI_3 [465 - 49] in the output above is a reverse-sense ORF running from position 465 to 49.

## Data files

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

The default file EGC.0 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 EGC.1.

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

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)
- ~/.embossdata

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

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

The format of these files is very simple.

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

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

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.

For example:

    ------------------------------------------------------------------------------
    # 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
    ------------------------------------------------------------------------------

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
marscan | Finds MAR/SAR sites in nucleic sequences
plotorf | Plot potential open reading frames
showorf | Pretty output of DNA translations
wobble | Wobble base plot

- checktrans - Reports STOP codons and ORF statistics of a protein sequence

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

2000 - written - Gary Williams

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments