| plotorf

## Function

Plot potential open reading frames

## Description

Plot potential open reading frames.

A graphical representation of where the open reading frames are in all 6 reading frames is shown. The ORFs are displayed as blue boxes.

ORFs in this program are defined as being regions between START and STOP codons.

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.

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
    Input sequence: tembl:paamir
    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
    Input sequence: ../../data/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

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
       -graph              xygraph    Graph type

       Optional qualifiers: (none)
       Advanced qualifiers:
       -start              string     Start codons
       -stop               string     Stop codons

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-graph" related qualifiers
       -gprompt             boolean    Graph prompting
       -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 standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence USA | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
Optional qualifiers | Allowed values | Default
(none)
Advanced 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:paamir' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:paamir

    ID   PAAMIR     standard; DNA; PRO; 2167 BP.
    XX
    AC   X13776; M43175;
    XX
    SV   X13776.1
    XX
    DT   19-APR-1989 (Rel. 19, Created)
    DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
    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; gamma subdivision; 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   MEDLINE; 89211409.
    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. 246:39-43(1989).
    XX
    RN   [3]
    RP   1-1292
    RX   MEDLINE; 91317707.
    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. 173:4914-4921(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   SWISS-PROT; P10932; AMIR_PSEAE.
    DR   SWISS-PROT; P27017; AMIC_PSEAE.
    DR   SWISS-PROT; Q51417; AMIS_PSEAE.

      [Part of this file has been deleted for brevity]

    FT                   phenotype"
    FT                   /replace=""
    FT                   /gene="amiC"
    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: ../../data/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]

    CATTGTCTTCTGCGCCTTCATCACTAGTCTAGTTCCCGCAATAGTATATCTTCACACAAACCAAGAAACACTCATCTCAA
    ACTGACACTGAATCACAATCCAAACCCTCAAACTAACACTTAGCTTTAAAATAGATTACTTTTCACTTATATTTATACCA
    GTAGCACTATTCATTACATGATCCATCATAGAATTCTCAATATGATATATGCACTCCGACCCCTACATCAACCAATTTTT
    TAAATACTTACTCCTCTTCCTCATCACCATACTAATCCTTGTTACAGCTAACAATCTCTTCCAACTTTTCATCGGATGAG
    AAGGAGTAGGAATTATATCCTTCTTACTAATTGGCTGATGATTCGGACGAACAGATGCAAATACAGCCGCCCTCCAAGCA
    ATCCTATACAATCGTATCGGAGACATTGGACTCCTTGCATCAATAGCATGATTTCTCTCTAATATAAACACATGAGACCT
    AGAACAAATCTTTATACTCAACCAAAACCCCTTAAATTTCCCCCTCATAGGACTCGTACTAGCCGCAGCAGGAAAATCGG
    CTCAATTCGGACTCCACCCTTGACTCCCATCAGCAATAGAAGGTCCTACCCCAGTCTCAGCCCTACTCCACTCAAGCACA
    ATAGTTGTAGCAGGAATCTTCTTGCTTGTCCGCTTCTACCCATTAATAGAAAATAACAAGCTAATCCAAACAGTAACCCT
    CTGCTTAGGCGCTATCACAACTCTATTTACAGCCATCTGTGCCCTCACCCAAAACGACATCAAAAAAATTATTGCTTTCT
    CCACCTCCAGCCAGCTAGGCCTAATAATAGTAACAATCGGCCTTAACCAACCTTACCTAGCATTCCTACACATTTGCACA
    CACGCCTTCTTTAAAGCTATACTATTCCTATGTTCTGGCTCCATCATCCATAACCTAAACAACGAACAAGATATCCGAAA
    AATAGGAGGGCTATTTAAGGCCCTCCCATTCACCACAACCGCCCTTATCATCGGATGTCTTGCACTAACAGGAATGCCAT
    TCCTGACCGGATTCTACTCCAAAGATCCCATTATTGAAGCCGCCACTTCGTCTTATACCAACGCCTGAGCCCTATTACTG
    ACCTTAATCGCCACCTCCCTTACGGCCGTCTATAGCACCCGCATCATTTTCTTTGCACTACTAGGACAACCCCGCTTCCC
    TCCCTCCACAACCATTAACGAAAATAATCCACTGTTAATCAACCCTATCAAACGACTACTCGTCGGAAGTATCTTCGCTG
    GCTTCATCCTATCCAACAGTATTCCCCCAATAACTACACCTTTAATAACCATACCCCTGCACTTAAAATTAACCGCCCTT
    GCAATAACAACCCTAGGCTTCATCATCGCATTCGAAATTAACCTTGACACACAAAATCTAAAGCACAAGCACCCATCAAA
    CTCCTTTAAATTCTCCACCTTACTAGGTTATTTCCCCACAATCATACATCGCCTACCCCCTCACCTTGACCTGTTAATAA
    GCCAAAAACTAGCAACTTCCCTACTAGATCTAACTTGACTAGAAACTATTTTACCAAAAACCACAGCCCTTATCCAACTA
    AAAGCCTCTACACTAACCTCTAACCAACAAGGCCTCATCAAACTCTACTTCTTATCTTTCCTCATCACCATCACCCTCAG
    CATAATCTTATTTAACTACCCCGAGTAATCTCCATAATAATTACAACACTAATAAATAAAGACCAACCCGTAACAATCAC
    CAACCAAACACCATAACTATATAATGCCGCAATCCCTGTAGCCTCCTCACTAAAAACCCCAGAACCCCCAGTATCATAAA
    CAACCCAGTCCCCTAGTCCATCAAACTCAAACATAATCTTCACCTCCCCACTCTTCAAAGCATAAATCACAATTAAAAAC
    TCCACCACCAACCCTAAAACAAATGCTCCTAGTACAACTTTATTAGAAACCCAAACCTCAGGATACTGTTCAGTAGCCAT
    AGCTGTTGTATAACCAAATACTACCAGCATTCCCCCCAAATAAATCAAAAACACCATTAACCCCAAAAACGAACCACCAA
    AACTCAAAATAACTCCACATCCAACACCACCACCCACAATCAACCCTAAACCCCCATAAATAGGTGAAGGCTTTGAAGAA
    ACCCCCACAAAACTAATTACAAAAATAATACTTAAAATGAAAACAATATACATTATCATTATTCTCACATGGACTTCAAC
    CATGACCAATGACATGAAAAATCATCGTTGTTATTCAACTACAAGAACACCAATGACCAACATCCGAAAAACACACCCAC
    TAATAAAAATCGTCAACGACGCATTCGTCGATCTCCCCACCCCATCAAATATCTCTTCATGATGGAACTTCGGCTCCCTA
    CTCGGCCTCTGCTTAATTATACAAATCCTAACAGGCCTATTCCTAGCAATACACTACACACCAGACACAACAACCGCCTT
    CTCATCAGTCACACACATCTGCCGAGACGTGAATTACGGCTGAATTATCCGATACCTACATGCAAATGGGGCTTCTATAT
    TCTTCATCTGCCTCTACGCTCACATAGGACGAGGCCTATACTACGGCTCCTACGCCTTCCGAGAAACATGAAATATTGGA
    GTTATTCTACTATTCACAGTTATAGCCACCGCATTCGTAGGCTACGTCCTGCCCTGAGGACAAATATCATTCTGAGGCGC
    AACTGTAATCACTAACCTCCTATCAGCAATCCCATACATTGGTACCACCCTAGTCGAATGAATCTGAGGCGGTTTCTCTG
    TAGATAAAGCAACACTAACACGCTTTTTTGCCTTTCACTTTATCCTCCCCTTCATCATCCTAGCATTAGCAATTGTCCAC
    CTTATTTTCCTTCACGAAACAGGATCCAACAACCCCACAGGCATCCCATCCGACATAGATAAAATCCCATTCCACCCCTA
    CCACACAATTAAAGACATTCTAGGTGCCCTATTACTAATCCTAATCCTACTAATACTAACCCTATTCGCACCCGACCTAC
    TTGGAGACCCAGACAACTATACCCCAGCAAACCCACTCAGTACCCCAGCACACATTAAACCAGAATGGTATTTTCTATTC
    GCATACGCAATCCTACGATCAATCCCCAACAAACTAGGCGGAGTCTTAGCCCTACTACTCTCAATCCTAATCCTAGCCTT
    CATCCCAATACTCCACACATCCAATCAACGAAGCATAATATTTCGACCCTTTAGCCAGTTCTTGTTCTGAGTCCTAGTCG
    CAGATCTACTAACCCTAACATGGATCGGCGGCCAACCAGTAGAACACCCCTACATAATTGTAGGCCAACTCGCATCCATC
    CTCTATTTCCTCTTAATTCTAGTATTAATACCAGTAACTAGTCTTATCGAGAACAAACTTATAAAATGAAGAGTCTTTGT
    AGTATAATTAAATACCCCGGTTTTGTAAACCGGAAAAGGAGACAAGACACACCTCCCTAAGACTCAAGGAAGAAGTATTA
    CACTCCACCATCAGCACCCAAAGCTGAAGTTCTACATAAACTATTCCCTGAAAAAGTATATTGTACAATAACCACAGGAC
    CACAGTACTATGTCCGTATTGAAAATAACTTGCCTTATTAGATATTATTATGTAACTCGTGCATGCATGTACTTCCACAT
    AATTAATAGCGTCTTTCCATGGGTATGAACAGATATACATGCTATGTATAATTGTGCATTCAATTATTTTCACCACGAGC
    AGTTGAAGCTCGTATTAAATTTTATTAATTTTACATATTACATAATATGTATTAATAGTACAATAGCGCATGTTCTTATG
    CATCCCCAGATCTATTTAAATCAAATGATTCCTATGGCCGCTCCATTAGATCACGAGCTTAGTCAGCATGCCGCGTGAAA
    CCAGCAACCCGCTTGGCAGGGATCCCTCTTCTCGCACCGGGCCCATCACTCGTGGGGGTAGCTATTTAATGATCTTTATA
    AGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTCGTTCCCCTTAAATAAGACATCTCGATGG

## 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

ORFs in this program are defined as being regions between START and STOP codons.

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

See the Notes section.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranseq | Back translate a protein sequence
coderet | Extract CDS, mRNA and translations from feature tables
getorf | Finds and extracts open reading frames (ORFs)
marscan | Finds MAR/SAR sites in nucleic sequences
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
showorf | Pretty output of DNA translations
showseq | Display a sequence with features, translation etc
sixpack | Display a DNA sequence with 6-frame translation and ORFs
syco | Synonymous codon usage Gribskov statistic plot
tcode | Fickett TESTCODE statistic to identify protein-coding DNA
transeq | Translate nucleic acid sequences
wobble | Wobble base plot

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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