
                                  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: 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   Sequence USA
   -graph              xygraph    Graph type

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

   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
   -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 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 deaths


   Standard (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, xml 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: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 Pseudomona
s
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 cause
s
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        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       90
0
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       96
0
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      102
0
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      108
0
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      114
0
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      120
0
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      126
0
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      132
0
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      138
0
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      144
0
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      150
0
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      156
0
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      162
0
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      168
0
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      174
0
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      180
0
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      186
0
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      192
0
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      198
0
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      204
0
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      210
0
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      216
0
     cctcgag                                                                216
7
//

  Input files for usage example 2

  File: mito.seq

>gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete geno
me
GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGC
T
TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATT
T
GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAA
C
TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGAC
A
GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACAT
G
AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAG
C
CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATC
C
CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCT
C
GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTT
A
AGGGTTGGTAAACTTCGTGCCAGCCACCGCGGTCATACGATCGACCCAAATTAATAGAAGCACGGCGTAAAGAGTGTTA
A
GGAGCCACATGAAATAAAGTCAAACCTTAATTAAGCTGTAAAAAGCCCTAATTAAAATTAAGCCAAACTACGAAAGTGA
C
TTTAATATAATCTGATCACACGACAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGTCGTAAACCCCAA
T
AGTCACAAAACAAGACTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTTGGCGGTGCCTCATACCC
A
TCTAGAGGAGCCTGTTCTGTAACCGATAAACCCCGATCAACCTCACCAACCCTTGCTACTTCAGTCTATATACCGCCAT
C
TTCAGCAAACCCTAAAGGGAGAAAAGTAAGCATAACCATCCTACATAAAAACGTTAGGTCAAGGTGTAACCCATGGGTT
G
GGAAGTAATGGGCTACATTTTCTAAGCTAAGAACATCCCCTATACTCACACGAAAGTTTTTATGAAACTTAAAAACTAA
A
GGAGGATTTAGTAGTAAATCAAGAGCAGAGTGCTTGATTGAATAAGGCCATGAGGGCACGCACACACCGCCCGTCACCC
T
CCTCAAGTACCCCAGCTATAAACCCCAGTTCGTTAACTCAGGCCAAGCAATTATACGAGAGGAGACAAGTCGTAACAAG
G
TAAGCATACCGGAAGGTGTGCTTGGACAAAACAAGATATAGCTTAAACAAAGCATGTAGTTTACACCTAGAAGATTCCA
C
AGCCCGTGTATATCTTGAACTAGCCCTAGCCCACACCCTCCCCACCTCTACTACCACAAATCAATCAAATAAAACATTT
A
CCATCCCTTCAAAGTATAGGAGATAGAAATTTAAATATCAGTGGCGCTATAGAGATAGTACCGTAAGGAAAGATGAAAG
A
AAAACCTAAAAGTAATAAAAAGCAAAGCTTACCACTTGTACCTTTTGCATAATGACTTAACTAGTAATAAATTAGCAAA
G
AGACCTTAAGTTAAATTACCCGAAACCAGACGAGCTACTTATGAGCAGCACCTAGAACGAACTCATCTATGTGGCAAAA
T
AGTGAGAAGACTTATAAGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTGTCCCTGAAAAGAATCTCAGTT
C
AACATTAAATAATACTAAAAGCCCATGCCAAGCCTTAACGTATATTTAACTGTTAATCTAAAAAGGTACAGCTTTTTAG
A
AATGGGTACAACCTTGACTAGAGAGTAAAATCAAACATAAACATAGTTGGCCTAAAAGCAGCCATCAATTAAGAAAGCG
T
TCAAGCTCGACAACAAAATAATGTTTTAATTCCAACATTAAGTAAATCAACTCCTAGCCTGACTATTGGACTAATCTAT
A
CAAATATAGAAGCAATACTGTTAATATGAGTAACAAGAAATTTTTCTCCTAGCACAAGCTTACACCAGTAACTGATAAT
A
TACTGATAATTAACAGCAAATAAATAAAACCCAACACTAAATTATTTATTAAAATACTGTTAACCCAACACAGGCGTGC
A
TTAAGGAAAGATTAAAAAAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCA
T
AACCAGTATTAGAGCACTGCCTGCCCGGTGACTAATCGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAA
T
CACTTGTTCTCTAATTAGGGACTTGTATGAATGGCCACACGAGGGTTTTACTGTCTCTTACTTTTAATCAGTGAAATTG
A
CCTCTCCGTGAAGAGGCGGAGATAACAAAATAAGACGAGAAGACCCTATGGAGCTTCAATTAATCAACCCAAAAACCAT
A
ACCTTAAACCACCAAGGGATAACAAAACCTTATATGGGCTGACAATTTCGGTTGGGGTGACCTCGGAGTACAAAAAACC
C
TCCGAGTGATTAAAACTTAGGCCCACTAGCCAAAGTACAATATCACTTATTGATCCAATCCTTTGATCAACGGAACAAG
T
TACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGATCAGGA
C
ATCCTAATGGTGCAGCTGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGT
A
ATCCAGGTCGGTTTCTATCTATTACGCATTTCTCCCAGTACGAAAGGACAAGAGAAATAAGGCCAACTTCAAACAAGCG
C
CTTCAAACAATTAATGACCTAGTCTCAACTTAATAATTAAGCGCAAACAAACCTGCCCAAGACCAGGGCCTTGTTGAGG
T
GGCAGAGTTCGGTAATTGCATAAAACTTAAACTTTTACACCCAGAGGTTCAAATCCTCTCCCCAACAAAATGTTTATAA
T
TAACATTCTAACACTCATTCTCCCCATCCTCCTAGCCGTAGCATTCCTAACGCTAGTAGAACGCAAAATTCTAGGCTAT
A
TGCAGTTCCGAAAGGGGCCAAACATCGTAGGCCCACATGGCTTACTCCAACCCTTTGCCGATGCAATTAAATTATTCAC
T
AAAGAACCCCTACGGCCAGCTACATCCTCAACTACTATGTTTATCATTGCACCAGTACTAGCCCTAACCCTGGCCCTCA
C
TATATGAAGCCCCCTACCCATACCATACCCCCTCATTAACATAAACCTAGGAGTATTATTCATATTAGCAATATCCAGC
C
TAGCCGTCTACTCCATCCTATGATCAGGCTGAGCCTCCAACTCAAAATACGCACTAATTGGAGCCCTACGAGCAGTAGC
A
CAAACAATCTCATATGAGGTAACACTAGCCATTATCCTCCTATCAGTACTCCTAATAAACGGCTCCTACACCTTATCAA
C
ATTAGCCACAACACAAGAACAACTATGATTACTATTCCCATCATGACCCTTAGCCATAATGTGATTCATCTCCACCCTA
G
CAGAAACTAATCGAGCTCCTTTTGATCTAACAGAGGGAGAATCAGAACTCGTATCAGGCTTCAACGTAGAATATGCAGC
A
GGCCCTTTCGCCCTATTCTTCCTGGCAGAATACGCCAACATCATTATAATGAATATACTCACAGCCATTTTATTCCTAG
G


  [Part of this file has been deleted for brevity]

CATTGTCTTCTGCGCCTTCATCACTAGTCTAGTTCCCGCAATAGTATATCTTCACACAAACCAAGAAACACTCATCTCA
A
ACTGACACTGAATCACAATCCAAACCCTCAAACTAACACTTAGCTTTAAAATAGATTACTTTTCACTTATATTTATACC
A
GTAGCACTATTCATTACATGATCCATCATAGAATTCTCAATATGATATATGCACTCCGACCCCTACATCAACCAATTTT
T
TAAATACTTACTCCTCTTCCTCATCACCATACTAATCCTTGTTACAGCTAACAATCTCTTCCAACTTTTCATCGGATGA
G
AAGGAGTAGGAATTATATCCTTCTTACTAATTGGCTGATGATTCGGACGAACAGATGCAAATACAGCCGCCCTCCAAGC
A
ATCCTATACAATCGTATCGGAGACATTGGACTCCTTGCATCAATAGCATGATTTCTCTCTAATATAAACACATGAGACC
T
AGAACAAATCTTTATACTCAACCAAAACCCCTTAAATTTCCCCCTCATAGGACTCGTACTAGCCGCAGCAGGAAAATCG
G
CTCAATTCGGACTCCACCCTTGACTCCCATCAGCAATAGAAGGTCCTACCCCAGTCTCAGCCCTACTCCACTCAAGCAC
A
ATAGTTGTAGCAGGAATCTTCTTGCTTGTCCGCTTCTACCCATTAATAGAAAATAACAAGCTAATCCAAACAGTAACCC
T
CTGCTTAGGCGCTATCACAACTCTATTTACAGCCATCTGTGCCCTCACCCAAAACGACATCAAAAAAATTATTGCTTTC
T
CCACCTCCAGCCAGCTAGGCCTAATAATAGTAACAATCGGCCTTAACCAACCTTACCTAGCATTCCTACACATTTGCAC
A
CACGCCTTCTTTAAAGCTATACTATTCCTATGTTCTGGCTCCATCATCCATAACCTAAACAACGAACAAGATATCCGAA
A
AATAGGAGGGCTATTTAAGGCCCTCCCATTCACCACAACCGCCCTTATCATCGGATGTCTTGCACTAACAGGAATGCCA
T
TCCTGACCGGATTCTACTCCAAAGATCCCATTATTGAAGCCGCCACTTCGTCTTATACCAACGCCTGAGCCCTATTACT
G
ACCTTAATCGCCACCTCCCTTACGGCCGTCTATAGCACCCGCATCATTTTCTTTGCACTACTAGGACAACCCCGCTTCC
C
TCCCTCCACAACCATTAACGAAAATAATCCACTGTTAATCAACCCTATCAAACGACTACTCGTCGGAAGTATCTTCGCT
G
GCTTCATCCTATCCAACAGTATTCCCCCAATAACTACACCTTTAATAACCATACCCCTGCACTTAAAATTAACCGCCCT
T
GCAATAACAACCCTAGGCTTCATCATCGCATTCGAAATTAACCTTGACACACAAAATCTAAAGCACAAGCACCCATCAA
A
CTCCTTTAAATTCTCCACCTTACTAGGTTATTTCCCCACAATCATACATCGCCTACCCCCTCACCTTGACCTGTTAATA
A
GCCAAAAACTAGCAACTTCCCTACTAGATCTAACTTGACTAGAAACTATTTTACCAAAAACCACAGCCCTTATCCAACT
A
AAAGCCTCTACACTAACCTCTAACCAACAAGGCCTCATCAAACTCTACTTCTTATCTTTCCTCATCACCATCACCCTCA
G
CATAATCTTATTTAACTACCCCGAGTAATCTCCATAATAATTACAACACTAATAAATAAAGACCAACCCGTAACAATCA
C
CAACCAAACACCATAACTATATAATGCCGCAATCCCTGTAGCCTCCTCACTAAAAACCCCAGAACCCCCAGTATCATAA
A
CAACCCAGTCCCCTAGTCCATCAAACTCAAACATAATCTTCACCTCCCCACTCTTCAAAGCATAAATCACAATTAAAAA
C
TCCACCACCAACCCTAAAACAAATGCTCCTAGTACAACTTTATTAGAAACCCAAACCTCAGGATACTGTTCAGTAGCCA
T
AGCTGTTGTATAACCAAATACTACCAGCATTCCCCCCAAATAAATCAAAAACACCATTAACCCCAAAAACGAACCACCA
A
AACTCAAAATAACTCCACATCCAACACCACCACCCACAATCAACCCTAAACCCCCATAAATAGGTGAAGGCTTTGAAGA
A
ACCCCCACAAAACTAATTACAAAAATAATACTTAAAATGAAAACAATATACATTATCATTATTCTCACATGGACTTCAA
C
CATGACCAATGACATGAAAAATCATCGTTGTTATTCAACTACAAGAACACCAATGACCAACATCCGAAAAACACACCCA
C
TAATAAAAATCGTCAACGACGCATTCGTCGATCTCCCCACCCCATCAAATATCTCTTCATGATGGAACTTCGGCTCCCT
A
CTCGGCCTCTGCTTAATTATACAAATCCTAACAGGCCTATTCCTAGCAATACACTACACACCAGACACAACAACCGCCT
T
CTCATCAGTCACACACATCTGCCGAGACGTGAATTACGGCTGAATTATCCGATACCTACATGCAAATGGGGCTTCTATA
T
TCTTCATCTGCCTCTACGCTCACATAGGACGAGGCCTATACTACGGCTCCTACGCCTTCCGAGAAACATGAAATATTGG
A
GTTATTCTACTATTCACAGTTATAGCCACCGCATTCGTAGGCTACGTCCTGCCCTGAGGACAAATATCATTCTGAGGCG
C
AACTGTAATCACTAACCTCCTATCAGCAATCCCATACATTGGTACCACCCTAGTCGAATGAATCTGAGGCGGTTTCTCT
G
TAGATAAAGCAACACTAACACGCTTTTTTGCCTTTCACTTTATCCTCCCCTTCATCATCCTAGCATTAGCAATTGTCCA
C
CTTATTTTCCTTCACGAAACAGGATCCAACAACCCCACAGGCATCCCATCCGACATAGATAAAATCCCATTCCACCCCT
A
CCACACAATTAAAGACATTCTAGGTGCCCTATTACTAATCCTAATCCTACTAATACTAACCCTATTCGCACCCGACCTA
C
TTGGAGACCCAGACAACTATACCCCAGCAAACCCACTCAGTACCCCAGCACACATTAAACCAGAATGGTATTTTCTATT
C
GCATACGCAATCCTACGATCAATCCCCAACAAACTAGGCGGAGTCTTAGCCCTACTACTCTCAATCCTAATCCTAGCCT
T
CATCCCAATACTCCACACATCCAATCAACGAAGCATAATATTTCGACCCTTTAGCCAGTTCTTGTTCTGAGTCCTAGTC
G
CAGATCTACTAACCCTAACATGGATCGGCGGCCAACCAGTAGAACACCCCTACATAATTGTAGGCCAACTCGCATCCAT
C
CTCTATTTCCTCTTAATTCTAGTATTAATACCAGTAACTAGTCTTATCGAGAACAAACTTATAAAATGAAGAGTCTTTG
T
AGTATAATTAAATACCCCGGTTTTGTAAACCGGAAAAGGAGACAAGACACACCTCCCTAAGACTCAAGGAAGAAGTATT
A
CACTCCACCATCAGCACCCAAAGCTGAAGTTCTACATAAACTATTCCCTGAAAAAGTATATTGTACAATAACCACAGGA
C
CACAGTACTATGTCCGTATTGAAAATAACTTGCCTTATTAGATATTATTATGTAACTCGTGCATGCATGTACTTCCACA
T
AATTAATAGCGTCTTTCCATGGGTATGAACAGATATACATGCTATGTATAATTGTGCATTCAATTATTTTCACCACGAG
C
AGTTGAAGCTCGTATTAAATTTTATTAATTTTACATATTACATAATATGTATTAATAGTACAATAGCGCATGTTCTTAT
G
CATCCCCAGATCTATTTAAATCAAATGATTCCTATGGCCGCTCCATTAGATCACGAGCTTAGTCAGCATGCCGCGTGAA
A
CCAGCAACCCGCTTGGCAGGGATCCCTCTTCTCGCACCGGGCCCATCACTCGTGGGGGTAGCTATTTAATGATCTTTAT
A
AGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTCGTTCCCCTTAAATAAGACATCTCGATGG

Output file format

  Output files for usage example

  Graphics File: plotorf.ps

   [plotorf results]

  Output files for usage example 2

  Graphics File: plotorf.ps

   [plotorf results]

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 © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   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

   None
