| sixpack

## Function

Display a DNA sequence with 6-frame translation and ORFs

## Description

sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the three forward and (optionally) three reverse translations in a pretty display format. A genetic code may be specified for the translation. There are various options to control the appearance of the output file. It also writes a file of protein sequences corresponding to any open reading frames that are larger than the specified minimum size: the default of 1 base shows all possible open reading frames.

## Algorithm

The program takes the following steps:

     The nucleic acid sequence is read in.
     The required genetic code is read in from the EGC* data files.
     The three forward and three reverse translations are created.
     The name and description are written to the ouput display file.
     Any required regions to be changed to upper case are changed.
     Any required regions to be highlighted in HTML colour tags are changed.
     The reverse sense sequence is placed below the forward sequence.
     The forward translations are placed above the sequences.
     The reverse translation are placed below the sequences.
     The display is written out, split at the ends of lines.
     Any ORFs that are longer than the specified minimum size are written to the output sequence file.

## Usage

Here is a sample session with sixpack

    % sixpack
    Display a DNA sequence with 6-frame translation and ORFs
    Input nucleotide sequence: tembl:x13776
    Output file [x13776.sixpack]:
    protein output sequence(s) [x13776.fasta]:

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)
      [-outfile]           outfile    [*.sixpack] Output file name
       -outseq             seqoutall  [.] ORF sequence output

       Additional (Optional) qualifiers:
       -table              menu       [0] Genetics code used for the translation
                                      (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))
       -[no]firstorf       boolean    [Y] Count the beginning of a sequence as a
                                      possible ORF, even if it's inferior to the
                                      minimal ORF size.
       -[no]lastorf        boolean    [Y] Count the end of a sequence as a
                                      possible ORF, even if it's not finishing
                                      with a STOP, or inferior to the minimal ORF
                                      size.
       -mstart             boolean    [N] Displays only ORFs starting with an M.

       Advanced (Unprompted) qualifiers:
       -[no]reverse        boolean    [Y] Display also the translation of the DNA
                                      sequence in the 3 reverse frames
       -orfminsize         integer    [1] Minimum size of Open Reading Frames
                                      (ORFs) to display in the translations.
                                      (Integer 1 or more)
       -uppercase          range      [If this is left blank, then the sequence
                                      case is left alone.] Regions to put in
                                      uppercase.
                                      If this is left blank, then the sequence
                                      case is left alone.
                                      A set of regions is specified by a set of
                                      pairs of positions.
                                      The positions are integers.
                                      They are separated by any non-digit,
                                      non-alpha character.
                                      Examples of region specifications are:
                                      24-45, 56-78
                                      1:45, 67=99;765..888
                                      1,5,8,10,23,45,57,99
       -highlight          range      [(full sequence)] Regions to colour if
                                      formatting for HTML.
                                      If this is left blank, then the sequence is
                                      left alone.
                                      A set of regions is specified by a set of
                                      pairs of positions.
                                      The positions are integers.
                                      They are followed by any valid HTML font
                                      colour.
                                      Examples of region specifications are:
                                      24-45 blue 56-78 orange
                                      1-100 green 120-156 red
                                      A file of ranges to colour (one range per
                                      line) can be specifed as '@filename'.
       -[no]number         boolean    [Y] Number the sequence at the beginning and
                                      the end of each line.
       -width              integer    [60] Number of nucleotides displayed on each
                                      line (Integer 1 or more)
       -length             integer    [0] Line length of page (0 for indefinite)
                                      (Integer 0 or more)
       -margin             integer    [10] Margin around sequence for numbering.
                                      (Integer 0 or more)
       -[no]name           boolean    [Y] Set this to be false if you do not wish
                                      to display the ID name of the sequence.
       -[no]description    boolean    [Y] Set this to be false if you do not wish
                                      to display the description of the sequence.
       -offset             integer    [1] Number from which you want the DNA
                                      sequence to be numbered. (Any integer value)
       -html               boolean    [N] Use HTML formatting

       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

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       "-outseq" associated qualifiers
       -osformat           string     Output seq format
       -osextension        string     File name extension
       -osname             string     Base file name
       -osdirectory        string     Output directory
       -osdbname           string     Database name to add
       -ossingle           boolean    Separate file for each entry
       -oufo               string     UFO features
       -offormat           string     Features format
       -ofname             string     Features file name
       -ofdirectory        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
[-outfile] (Parameter 2) | Output file name | Output file | <*>.sixpack
-outseq | ORF sequence output | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers | Allowed values | Default
-table | Genetics code used for the translation |
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
-[no]firstorf | Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size. | Boolean value Yes/No | Yes
-[no]lastorf | Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size. | Boolean value Yes/No | Yes
-mstart | Displays only ORFs starting with an M. | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers | Allowed values | Default
-[no]reverse | Display also the translation of the DNA sequence in the 3 reverse frames | Boolean value Yes/No | Yes
-orfminsize | Minimum size of Open Reading Frames (ORFs) to display in the translations. | Integer 1 or more | 1
-uppercase | Regions to put in uppercase. If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 | Sequence range | If this is left blank, then the sequence case is left alone.
-highlight | Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specifed as '@filename'. | Sequence range | full sequence
-[no]number | Number the sequence at the beginning and the end of each line. | Boolean value Yes/No | Yes
-width | Number of nucleotides displayed on each line | Integer 1 or more | 60
-length | Line length of page (0 for indefinite) | Integer 0 or more | 0
-margin | Margin around sequence for numbering. | Integer 0 or more | 10
-[no]name | Set this to be false if you do not wish to display the ID name of the sequence. | Boolean value Yes/No | Yes
-[no]description | Set this to be false if you do not wish to display the description of the sequence. | Boolean value Yes/No | Yes
-offset | Number from which you want the DNA sequence to be numbered. | Any integer value | 1
-html | Use HTML formatting | Boolean value Yes/No | No

## Input file format

sixpack reads any normal sequence USAs.

### 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
    //

## Output file format

### Output files for usage example

### File: x13776.sixpack

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation

              G  T  A  G  R  A  S  A  R  S  P  P  A  G  R  R  E  L  H  D     F1
               V  P  L  A  E  H  L  L  D  H  H  Q  P  G  D  G  N  C  T  I    F2
                Y  R  W  P  S  I  C  S  I  T  T  S  R  A  T  G  T  A  R  S   F3
            1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60
              ----:----|----:----|----:----|----:----|----:----|----:----|
            1 ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta 60
               P  V  A  P  R  A  D  A  R  D  G  G  A  P  R  R  S  S  C  S    F6
              X  Y  R  Q  G  L  M  Q  E  I  V  V  L  R  A  V  P  V  A  R     F5
                T  G  S  A  S  C  R  S  S  *  W  W  G  P  S  P  F  Q  V  I   F4

              L  P  G  E  P  G  A  R  A  G  S  L  R  T  A  L  S  D  S  H     F1
               Y  L  A  S  L  E  H  E  R  V  R  F  V  R  R  *  A  T  V  T    F2
                T  W  R  A  W  S  T  S  G  F  A  S  Y  G  A  E  R  Q  S  Q   F3
           61 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 120
              ----:----|----:----|----:----|----:----|----:----|----:----|
           61 gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg 120
               R  G  P  S  G  P  A  R  A  P  E  S  R  V  A  S  L  S  L  *    F6
              D  V  Q  R  A  Q  L  V  L  P  N  A  E  Y  P  A  S  R  C  D     F5
                *  R  A  L  R  S  C  S  R  T  R  K  T  R  R  Q  A  V  T  V   F4

              R  R  G  N  G  W  D  R  T  R  S  G  R  *  S  A  C  C  S  P     F1
               G  E  E  T  D  G  I  A  P  G  A  A  A  D  R  P  A  V  L  R    F2
                E  R  K  R  M  G  S  H  Q  E  R  P  L  I  G  L  L  F  S  E   F3
          121 aggagaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180
              ----:----|----:----|----:----|----:----|----:----|----:----|
          121 tcctctcctttgcctaccctagcgtggtcctcgccggcgactagccggacgacaagaggc 180
               L  L  P  F  P  H  S  R  V  L  L  P  R  Q  D  A  Q  Q  E  G    F6
              C  S  L  F  R  I  P  D  C  W  S  R  G  S  I  P  R  S  N  E     F5
                P  S  S  V  S  P  I  A  G  P  A  A  A  S  R  G  A  T  R  R   F4

              K  P  A  S  P  P  I  S  S  A  R  T  R  M  A  H  C  S  R  S     F1
               N  R  R  H  R  R  Y  R  A  L  A  R  V  W  R  I  A  R  G  R    F2
                T  G  V  T  A  D  I  E  R  S  H  A  Y  G  A  L  L  A  V  E   F3
          181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240
              ----:----|----:----|----:----|----:----|----:----|----:----|
          181 tttggccgcagtggcggctatagctcgcgagcgtgcgcataccgcgtaacgagcgccagc 240
               F  G  A  D  G  G  I  D  L  A  R  V  R  I  A  C  Q  E  R  D    F6
              S  V  P  T  V  A  S  I  S  R  E  C  A  Y  P  A  N  S  A  T     F5
                F  R  R  *  R  R  Y  R  A  S  A  R  T  H  R  M  A  R  P  R   F4

              S  N  *  T  A  R  A  A  S  A  V  A  R  S  K  R  C  P  R  T     F1

      [Part of this file has been deleted for brevity]

         1981 caacgacccgttctagtcgccagccctccaccgccactagttgaaggaccagccgcacga 2040
               T  A  P  C  S  *  R  D  P  P  P  P  S  *  S  G  P  R  R  A    F6
              P  Q  Q  A  L  D  A  T  P  L  H  R  H  D  V  E  Q  D  A  H     F5
                N  S  P  L  I  L  P  R  S  T  A  T  I  L  K  R  T  P  T  S   F4

              E  R  L  R  R  V  L  P  D  L  F  R  S  S  R  A  G  L  A  E     F1
               S  A  C  V  A  F  Y  L  I  F  S  A  A  A  G  Q  G  S  L  K    F2
                A  P  A  S  R  S  T  *  S  F  P  Q  Q  P  G  R  A  R  *  R   F3
         2041 gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100
              ----:----|----:----|----:----|----:----|----:----|----:----|
         2041 ctcgcggacgcagcgcaagatggactagaaaaggcgtcgtcggcccgtcccgagcgactt 2100
               S  R  R  R  R  T  R  G  S  R  K  R  L  L  R  A  P  S  A  S    F6
              Q  A  G  A  D  R  E  V  Q  D  K  G  C  C  G  P  L  A  R  Q     F5
                L  A  Q  T  A  N  *  R  I  K  E  A  A  A  P  C  P  E  S  F   F4

              G  R  S  A  D  P  A  I  R  F  Y  L  S  V  G  G  R  Q  P  V     F1
               A  G  A  L  T  L  L  F  A  F  T  Y  L  W  V  A  A  N  Q  F    F2
                P  E  R  *  P  C  Y  S  L  L  P  I  C  G  W  P  P  T  S  S   F3
         2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt 2160
              ----:----|----:----|----:----|----:----|----:----|----:----|
         2101 ccggcctcgcgactgggacgataagcgaaaatggatagacacccaccggcggttggtcaa 2160
               P  R  L  A  S  G  A  I  R  K  *  R  D  T  P  P  R  W  G  T    F6
              L  G  S  R  Q  G  Q  *  E  S  K  G  I  Q  P  H  G  G  V  L     F5
                A  P  A  S  V  R  S  N  A  K  V  *  R  H  T  A  A  L  W  N   F4

              P  R  X                                                        F1
               L  E                                                          F2
                S  X                                                         F3
         2161 cctcgag 2167
              ----:--
         2161 ggagctc 2220
               G  R                                                          F6
              E  E  L                                                        F5
                R  S                                                         F4

    ##############################
    Minimum size of ORFs : 1

    Total ORFs in frame 1 :     8
    Total ORFs in frame 2 :     5
    Total ORFs in frame 3 :    13
    Total ORFs in frame 4 :    10
    Total ORFs in frame 5 :    16
    Total ORFs in frame 6 :    15

    Total ORFs :    67
    ##############################

### File: x13776.fasta

    >X13776_1_ORF1  Translation of X13776 in frame 1, ORF 1, threshold 1, 53aa
    GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR
    >X13776_1_ORF2  Translation of X13776 in frame 1, ORF 2, threshold 1, 28aa
    SACCSPKPASPPISSARTRMAHCSRSSN
    >X13776_1_ORF3  Translation of X13776 in frame 1, ORF 3, threshold 1, 52aa
    TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR
    >X13776_1_ORF4  Translation of X13776 in frame 1, ORF 4, threshold 1, 43aa
    CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT
    >X13776_1_ORF5  Translation of X13776 in frame 1, ORF 5, threshold 1, 23aa
    FATTASGWCSSARTTSIRGKATM
    >X13776_1_ORF6  Translation of X13776 in frame 1, ORF 6, threshold 1, 72aa
    CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV
    ATATAGGRRSPA
    >X13776_1_ORF7  Translation of X13776 in frame 1, ORF 7, threshold 1, 357aa
    PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR
    PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR
    SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP
    GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV
    RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP
    DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ
    >X13776_1_ORF8  Translation of X13776 in frame 1, ORF 8, threshold 1, 88aa
    QEGYRHHAGTGSAVRWRGAVSQCRLVAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSR
    AGLAEGRSADPAIRFYLSVGGRQPVPRX
    >X13776_2_ORF1  Translation of X13776 in frame 2, ORF 1, threshold 1, 35aa
    VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR
    >X13776_2_ORF2  Translation of X13776 in frame 2, ORF 2, threshold 1, 252aa
    ATVTGEETDGIAPGAAADRPAVLRNRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNA
    VPGPRRRPGPLSAVRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLR
    VFAEHRLRRSGAEPEQCAAGGVPDSPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGA
    RGNLHSAVSLRRRLAARRRAHLPGARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQP
    DHQRGGGGEDGE
    >X13776_2_ORF3  Translation of X13776 in frame 2, ORF 3, threshold 1, 125aa
    RGRGAGGGRALLLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQ
    LAGGRRAAAPVRHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRP
    LCRRA
    >X13776_2_ORF4  Translation of X13776 in frame 2, ORF 4, threshold 1, 210aa
    PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP
    EAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVI
    TQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDERE
    AHQHLSREAMKRREPILKIAQELLGNEPSA
    >X13776_2_ORF5  Translation of X13776 in frame 2, ORF 5, threshold 1, 96aa
    AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVWLLGKISGREVAVINFLVGVLSACVAF
    YLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQFLE
    >X13776_3_ORF1  Translation of X13776 in frame 3, ORF 1, threshold 1, 429aa
    YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE
    TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV
    RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI
    RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA
    RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY
    FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY

      [Part of this file has been deleted for brevity]

    SEPMNTTRSP
    >X13776_5_ORF11  Translation of X13776 in frame 5, ORF 11, threshold 1, 19aa
    WRIRYAASGALFWFGAGPP
    >X13776_5_ORF12  Translation of X13776 in frame 5, ORF 12, threshold 1, 10aa
    TMFGEYSKPS
    >X13776_5_ORF13  Translation of X13776 in frame 5, ORF 13, threshold 1, 3aa
    GVG
    >X13776_5_ORF14  Translation of X13776 in frame 5, ORF 14, threshold 1, 20aa
    QSSASARSTTGITALRVCDM
    >X13776_5_ORF15  Translation of X13776 in frame 5, ORF 15, threshold 1, 19aa
    QPTRNRTPRLRMKSSAHSR
    >X13776_5_ORF16  Translation of X13776 in frame 5, ORF 16, threshold 1, 107aa
    RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVTPVSENSRPISGRSWCD
    PIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQRYX
    >X13776_6_ORF1  Translation of X13776 in frame 6, ORF 1, threshold 1, 11aa
    RGTGWRPPTDR
    >X13776_6_ORF2  Translation of X13776 in frame 6, ORF 2, threshold 1, 36aa
    KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS
    >X13776_6_ORF3  Translation of X13776 in frame 6, ORF 3, threshold 1, 7aa
    SPPPPDR
    >X13776_6_ORF4  Translation of X13776 in frame 6, ORF 4, threshold 1, 8aa
    SCPATRRH
    >X13776_6_ORF5  Translation of X13776 in frame 6, ORF 5, threshold 1, 14aa
    ETAPRQRTAEPVPA
    >X13776_6_ORF6  Translation of X13776 in frame 6, ORF 6, threshold 1, 61aa
    RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLPATGAGAPRARPSHGAASATPWP
    G
    >X13776_6_ORF7  Translation of X13776 in frame 6, ORF 7, threshold 1, 23aa
    SGPGRRCGPGAARSSASASPFPR
    >X13776_6_ORF8  Translation of X13776 in frame 6, ORF 8, threshold 1, 18aa
    CAAPIPAQAAPGGHRAAG
    >X13776_6_ORF9  Translation of X13776 in frame 6, ORF 9, threshold 1, 8aa
    SRRGTPAR
    >X13776_6_ORF10  Translation of X13776 in frame 6, ORF 10, threshold 1, 16aa
    SARAPRGFRTPPAPPG
    >X13776_6_ORF11  Translation of X13776 in frame 6, ORF 11, threshold 1, 22aa
    CAESRRRAAQRSRRGGHSGKCW
    >X13776_6_ORF12  Translation of X13776 in frame 6, ORF 12, threshold 1, 32aa
    RPRPPARRRLPAAASTGAPNNRCGSAARPGRR
    >X13776_6_ORF13  Translation of X13776 in frame 6, ORF 13, threshold 1, 5aa
    PPPAG
    >X13776_6_ORF14  Translation of X13776 in frame 6, ORF 14, threshold 1, 407aa
    GPAPATRAGCRAASWRSWERSPAHAGGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFR
    DARRQAAVVVLALHPDRPLWRVDVDVVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGG
    DGRVLREETMAGLDEGPAGGRIDAGEVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAV
    AVATGDGAIQLGGAGAHHGGEDHVGARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQ
    VAHHMVAFPRIDVVRADEHHPLAVVANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVA
    EQRVGALDHRHHRLARVRHVAAHEEPYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADA
    ALAVQLLDREQCAIRVRALDIGGDAGFGEQQADQRPLLVRSHPFPLL
    >X13776_6_ORF15  Translation of X13776 in frame 6, ORF 15, threshold 1, 39aa
    LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPAVP

## Data files

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

An open reading frame is defined in this program as any possible translation between two STOP codons. Optionally, the beginning or end of a sequence may be counted as an ORF even if it's less than the minimal ORF size or (end only) lacking a STOP codon. See the -firstorf and -lastorf options.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Display the trace in an ABI sequencer file
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
cirdna | Draws circular maps of DNA constructs
coderet | Extract CDS, mRNA and translations from feature tables
getorf | Finds and extracts open reading frames (ORFs)
lindna | Draws linear maps of DNA constructs
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
pepnet | Draw a helical net for a protein sequence
pepwheel | Draw a helical wheel diagram for a protein sequence
plotorf | Plot potential open reading frames in a nucleotide sequence
prettyplot | Draw a sequence alignment with pretty formatting
prettyseq | Write a nucleotide sequence and its translation to file
remap | Display restriction enzyme binding sites in a nucleotide sequence
seealso | Finds programs with similar function to a specified program
showalign | Display a multiple sequence alignment in pretty format
showdb | Displays information on configured databases
showfeat | Display features of a sequence in pretty format
showorf | Display a nucleotide sequence and translation in pretty format
showseq | Displays sequences with features in pretty format
syco | Draw synonymous codon usage statictic plot for a nucleotide sequence
tcode | Identify protein-coding regions using Fickett TESTCODE statistic
textsearch | Search the textual description of sequence(s)
transeq | Translate nucleic acid sequences
wobble | Plot third base position variability in a nucleotide sequence

## Author(s)

Thomas Laurent (thomas.laurent © uk.lionbioscience.com)
Lion Bioscience Ltd, Compass House, 80-82 Newmarket Road, Cambridge, CB5 8DZ, UK

## History

Written (November 2002) - Thomas Laurent

## Target users

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

## Comments

None