EMBOSS: plotorf

| plotorf

## Function

Plot potential open reading frames in a nucleotide sequence

## Description

plotorf plots potential open reading frames (ORFs) for an input nucleotide sequence. ORFs in this program are defined as being regions between the specified START and STOP codons. A graphical representation of where the open reading frames are in all 6 reading frames is shown. The ORFs are displayed as blue boxes.

## Algorithm

ORFs in this program are defined as being regions between START and STOP codons. The default START codon is: `ATG`. The default STOP codons are: `TAA`,`TAG`,`TGA`. You can specify your own set of start and stop codons using the `-start` and `-stop` qualifiers.

## Usage

Here is a sample session with plotorf

    % plotorf
    Plot potential open reading frames in a nucleotide sequence
    Input nucleotide sequence: tembl:x13776
    Graph type [x11]: cps

    Created plotorf.ps

Go to the input files for this example
Go to the output files for this example

Example 2

An example of specifying your own START and STOP codons with a mitochondrial sequence would be:

    % plotorf -start ATT,ATC,ATA,ATG,GTG -stop TAA,TAG,AGA,AGG
    Plot potential open reading frames in a nucleotide sequence
    Input nucleotide sequence: mito.seq
    Graph type [x11]: cps

    Created plotorf.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Nucleotide sequence filename and optional
                                      format, or reference (input USA)
       -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -start              string     [ATG] Start codons (Any string is accepted)
       -stop               string     [TAA,TAG,TGA] Stop codons (Any string is
                                      accepted)

       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

       "-graph" associated qualifiers
       -gprompt            boolean    Graph prompting
       -gdesc              string     Graph description
       -gtitle             string     Graph title
       -gsubtitle          string     Graph subtitle
       -gxtitle            string     Graph x axis title
       -gytitle            string     Graph y axis title
       -goutfile           string     Output file for non interactive displays
       -gdirectory         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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
-start | Start codons | Any string is accepted | ATG
-stop | Stop codons | Any string is accepted | TAA,TAG,TGA

## Input file format

Any nucleic acid sequence.

### Input files for usage example

'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x13776

    ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
    XX
    AC   X13776; M43175;
    XX
    DT   19-APR-1989 (Rel. 19, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
    XX
    DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
    XX
    KW   aliphatic amidase regulator; amiC gene; amiR gene.
    XX
    OS   Pseudomonas aeruginosa
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
    OC   Pseudomonadaceae; Pseudomonas.
    XX
    RN   [1]
    RP   1167-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    RN   [2]
    RP   1167-2167
    RX   DOI; 10.1016/0014-5793(89)80249-2.
    RX   PUBMED; 2495988.
    RA   Lowe N., Rice P.M., Drew R.E.;
    RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
    RT   aeruginosa";
    RL   FEBS Lett. 246(1-2):39-43(1989).
    XX
    RN   [3]
    RP   1-1292
    RX   PUBMED; 1907262.
    RA   Wilson S., Drew R.;
    RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
    RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
    RT   product.";
    RL   J. Bacteriol. 173(16):4914-4921(1991).
    XX
    RN   [4]
    RP   1-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    DR   GOA; Q51417.
    DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
    XX

      [Part of this file has been deleted for brevity]

    FT                   /replace=""
    FT                   /note="ClaI fragment deleted in pSW36,  constitutive
    FT                   phenotype"
    FT   misc_feature    1
    FT                   /note="last base of an XhoI site"
    FT   misc_feature    648..653
    FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
    FT                   constitutive expression of amiE"
    FT   conflict        1281
    FT                   /replace="g"
    FT                   /citation=[3]
    XX
    SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
         ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
         ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
         aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
         aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
         agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
         ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
         tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
         agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
         acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
         ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
         gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
         acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
         cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
         ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
         aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
         acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
         tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
         tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
         acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
         gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
         agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
         ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
         cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
         gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
         gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
         gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
         cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
         tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
         gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
         ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
         gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
         aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
         catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
         gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
         gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
         ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
         cctcgag                                                                2167
    //

### Input files for usage example 2

### File: mito.seq

    >gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete genome
    GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGCT
    TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATTT
    GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAAC
    TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGACA
    GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACATG
    AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAGC
    CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATCC
    CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCTC
    GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTTA
    AGGGTTGGTAAACTTCGTGCCAGCCACCGCGGTCATACGATCGACCCAAATTAATAGAAGCACGGCGTAAAGAGTGTTAA
    GGAGCCACATGAAATAAAGTCAAACCTTAATTAAGCTGTAAAAAGCCCTAATTAAAATTAAGCCAAACTACGAAAGTGAC
    TTTAATATAATCTGATCACACGACAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGTCGTAAACCCCAAT
    AGTCACAAAACAAGACTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTTGGCGGTGCCTCATACCCA
    TCTAGAGGAGCCTGTTCTGTAACCGATAAACCCCGATCAACCTCACCAACCCTTGCTACTTCAGTCTATATACCGCCATC
    TTCAGCAAACCCTAAAGGGAGAAAAGTAAGCATAACCATCCTACATAAAAACGTTAGGTCAAGGTGTAACCCATGGGTTG
    GGAAGTAATGGGCTACATTTTCTAAGCTAAGAACATCCCCTATACTCACACGAAAGTTTTTATGAAACTTAAAAACTAAA
    GGAGGATTTAGTAGTAAATCAAGAGCAGAGTGCTTGATTGAATAAGGCCATGAGGGCACGCACACACCGCCCGTCACCCT
    CCTCAAGTACCCCAGCTATAAACCCCAGTTCGTTAACTCAGGCCAAGCAATTATACGAGAGGAGACAAGTCGTAACAAGG
    TAAGCATACCGGAAGGTGTGCTTGGACAAAACAAGATATAGCTTAAACAAAGCATGTAGTTTACACCTAGAAGATTCCAC
    AGCCCGTGTATATCTTGAACTAGCCCTAGCCCACACCCTCCCCACCTCTACTACCACAAATCAATCAAATAAAACATTTA
    CCATCCCTTCAAAGTATAGGAGATAGAAATTTAAATATCAGTGGCGCTATAGAGATAGTACCGTAAGGAAAGATGAAAGA
    AAAACCTAAAAGTAATAAAAAGCAAAGCTTACCACTTGTACCTTTTGCATAATGACTTAACTAGTAATAAATTAGCAAAG
    AGACCTTAAGTTAAATTACCCGAAACCAGACGAGCTACTTATGAGCAGCACCTAGAACGAACTCATCTATGTGGCAAAAT
    AGTGAGAAGACTTATAAGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTGTCCCTGAAAAGAATCTCAGTTC
    AACATTAAATAATACTAAAAGCCCATGCCAAGCCTTAACGTATATTTAACTGTTAATCTAAAAAGGTACAGCTTTTTAGA
    AATGGGTACAACCTTGACTAGAGAGTAAAATCAAACATAAACATAGTTGGCCTAAAAGCAGCCATCAATTAAGAAAGCGT
    TCAAGCTCGACAACAAAATAATGTTTTAATTCCAACATTAAGTAAATCAACTCCTAGCCTGACTATTGGACTAATCTATA
    CAAATATAGAAGCAATACTGTTAATATGAGTAACAAGAAATTTTTCTCCTAGCACAAGCTTACACCAGTAACTGATAATA
    TACTGATAATTAACAGCAAATAAATAAAACCCAACACTAAATTATTTATTAAAATACTGTTAACCCAACACAGGCGTGCA
    TTAAGGAAAGATTAAAAAAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCAT
    AACCAGTATTAGAGCACTGCCTGCCCGGTGACTAATCGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAAT
    CACTTGTTCTCTAATTAGGGACTTGTATGAATGGCCACACGAGGGTTTTACTGTCTCTTACTTTTAATCAGTGAAATTGA
    CCTCTCCGTGAAGAGGCGGAGATAACAAAATAAGACGAGAAGACCCTATGGAGCTTCAATTAATCAACCCAAAAACCATA
    ACCTTAAACCACCAAGGGATAACAAAACCTTATATGGGCTGACAATTTCGGTTGGGGTGACCTCGGAGTACAAAAAACCC
    TCCGAGTGATTAAAACTTAGGCCCACTAGCCAAAGTACAATATCACTTATTGATCCAATCCTTTGATCAACGGAACAAGT
    TACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGATCAGGAC
    ATCCTAATGGTGCAGCTGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTA
    ATCCAGGTCGGTTTCTATCTATTACGCATTTCTCCCAGTACGAAAGGACAAGAGAAATAAGGCCAACTTCAAACAAGCGC
    CTTCAAACAATTAATGACCTAGTCTCAACTTAATAATTAAGCGCAAACAAACCTGCCCAAGACCAGGGCCTTGTTGAGGT
    GGCAGAGTTCGGTAATTGCATAAAACTTAAACTTTTACACCCAGAGGTTCAAATCCTCTCCCCAACAAAATGTTTATAAT
    TAACATTCTAACACTCATTCTCCCCATCCTCCTAGCCGTAGCATTCCTAACGCTAGTAGAACGCAAAATTCTAGGCTATA
    TGCAGTTCCGAAAGGGGCCAAACATCGTAGGCCCACATGGCTTACTCCAACCCTTTGCCGATGCAATTAAATTATTCACT
    AAAGAACCCCTACGGCCAGCTACATCCTCAACTACTATGTTTATCATTGCACCAGTACTAGCCCTAACCCTGGCCCTCAC
    TATATGAAGCCCCCTACCCATACCATACCCCCTCATTAACATAAACCTAGGAGTATTATTCATATTAGCAATATCCAGCC
    TAGCCGTCTACTCCATCCTATGATCAGGCTGAGCCTCCAACTCAAAATACGCACTAATTGGAGCCCTACGAGCAGTAGCA
    CAAACAATCTCATATGAGGTAACACTAGCCATTATCCTCCTATCAGTACTCCTAATAAACGGCTCCTACACCTTATCAAC
    ATTAGCCACAACACAAGAACAACTATGATTACTATTCCCATCATGACCCTTAGCCATAATGTGATTCATCTCCACCCTAG
    CAGAAACTAATCGAGCTCCTTTTGATCTAACAGAGGGAGAATCAGAACTCGTATCAGGCTTCAACGTAGAATATGCAGCA
    GGCCCTTTCGCCCTATTCTTCCTGGCAGAATACGCCAACATCATTATAATGAATATACTCACAGCCATTTTATTCCTAGG

      [Part of this file has been deleted for brevity]

    [encoded data, 4129 characters]

## Output file format

### Output files for usage example

### Graphics File: plotorf.ps

### Output files for usage example 2

### Graphics File: plotorf.ps

## Data files

None.

## Notes

Note that this definition of an ORF would miss those exons in eukaryotic genomic sequences which do not contain a START codon. plotorf is only really useful when dealing with prokaryotic or mRNA eukaryotic sequences.

## References

None.

## Warnings

ORFs in this program are defined as being regions between START and STOP codons. This definition would miss those exons in eukaryotic genomic sequences which do not contain a START codon. plotorf is therefore only really useful when dealing with prokaryotic or mRNA eukaryotic sequences.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
coderet | Extract CDS, mRNA and translations from feature tables
getorf | Finds and extracts open reading frames (ORFs)
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
prettyseq | Write a nucleotide sequence and its translation to file
remap | Display restriction enzyme binding sites in a nucleotide sequence
showorf | Display a nucleotide sequence and translation in pretty format
showseq | Displays sequences with features in pretty format
sixpack | Display a DNA sequence with 6-frame translation and ORFs
syco | Draw synonymous codon usage statictic plot for a nucleotide sequence
tcode | Identify protein-coding regions using Fickett TESTCODE statistic
transeq | Translate nucleic acid sequences
wobble | Plot third base position variability in a nucleotide sequence

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

Written (1999) - Alan Bleasby

## Target users

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

## Comments

None