| sixpack

## Function

Display a DNA sequence with 6-frame translation and ORFs

## Description

sixpack takes a nucleic acid sequence and writes out the forward and reverse senses of the sequence with the 3 forward and three reverse translations in a pretty display format.

It also writes a file containing the open reading frames that are larger than the specified minimum size (default 1 base, showing all possible open reading frames). These open reading frames are written as protein sequences in the default output sequence format.

An open reading frame is defined in this program as any possible translation between two STOP codons.

## Algorithm

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 sequence: tembl:paamir
    Output file [paamir.sixpack]:
    Output sequence [paamir.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   Sequence USA
      [-outfile]           outfile    Output file name
       -outseq             seqoutall  ORF sequence output

       Additional (Optional) qualifiers:
       -table              menu       Genetics code used for the translation
       -[no]firstorf       boolean    Count the beginning of a sequence as a
                                      possible ORF, even if it's inferior to the
                                      minimal ORF size.
       -[no]lastorf        boolean    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    Displays only ORFs starting with an M.

       Advanced (Unprompted) qualifiers:
       -[no]reverse        boolean    Display also the translation of the DNA
                                      sequence in the 3 reverse frames
       -orfminsize         integer    Minimum size of Open Reading Frames (ORFs)
                                      to display in the translations.
       -uppercase          range      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      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    Number the sequence at the beginning and the
                                      end of each line.
       -width              integer    Number of nucleotides displayed on each line
       -length             integer    Line length of page (0 for indefinite)
       -margin             integer    Margin around sequence for numbering.
       -[no]name           boolean    Set this to be false if you do not wish to
                                      display the ID name of the sequence.
       -[no]description    boolean    Set this to be false if you do not wish to
                                      display the description of the sequence.
       -offset             integer    Number from which you want the DNA sequence
                                      to be numbered.
       -html               boolean    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 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
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.sixpack
-outseq | ORF sequence output | Writeable sequence(s) | <sequence>.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: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
    //

## Output file format

### Output files for usage example

### File: paamir.sixpack

    PAAMIR
    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                                                            F3
         2161 cctcgag                                                      2167
              ----:----|----:----|----:----|----:----|----:----|----:----|
         2161 ggagctc                                                      2167
               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: paamir.fasta

    >PAAMIR_1_ORF1  Translation of PAAMIR in frame 1, ORF 1, threshold 1, 53aa
    GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR
    >PAAMIR_1_ORF2  Translation of PAAMIR in frame 1, ORF 2, threshold 1, 28aa
    SACCSPKPASPPISSARTRMAHCSRSSN
    >PAAMIR_1_ORF3  Translation of PAAMIR in frame 1, ORF 3, threshold 1, 52aa
    TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR
    >PAAMIR_1_ORF4  Translation of PAAMIR in frame 1, ORF 4, threshold 1, 43aa
    CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT
    >PAAMIR_1_ORF5  Translation of PAAMIR in frame 1, ORF 5, threshold 1, 23aa
    FATTASGWCSSARTTSIRGKATM
    >PAAMIR_1_ORF6  Translation of PAAMIR in frame 1, ORF 6, threshold 1, 72aa
    CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV
    ATATAGGRRSPA
    >PAAMIR_1_ORF7  Translation of PAAMIR in frame 1, ORF 7, threshold 1, 357aa
    PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR
    PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR
    SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP
    GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV
    RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP
    DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ
    >PAAMIR_1_ORF8  Translation of PAAMIR in frame 1, ORF 8, threshold 1, 88aa
    QEGYRHHAGTGSAVRWRGAVSQCRLVAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSR
    AGLAEGRSADPAIRFYLSVGGRQPVPRX
    >PAAMIR_2_ORF1  Translation of PAAMIR in frame 2, ORF 1, threshold 1, 35aa
    VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR
    >PAAMIR_2_ORF2  Translation of PAAMIR in frame 2, ORF 2, threshold 1, 252aa
    ATVTGEETDGIAPGAAADRPAVLRNRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNA
    VPGPRRRPGPLSAVRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLR
    VFAEHRLRRSGAEPEQCAAGGVPDSPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGA
    RGNLHSAVSLRRRLAARRRAHLPGARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQP
    DHQRGGGGEDGE
    >PAAMIR_2_ORF3  Translation of PAAMIR in frame 2, ORF 3, threshold 1, 125aa
    RGRGAGGGRALLLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQ
    LAGGRRAAAPVRHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRP
    LCRRA
    >PAAMIR_2_ORF4  Translation of PAAMIR in frame 2, ORF 4, threshold 1, 210aa
    PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP
    EAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVI
    TQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDERE
    AHQHLSREAMKRREPILKIAQELLGNEPSA
    >PAAMIR_2_ORF5  Translation of PAAMIR in frame 2, ORF 5, threshold 1, 96aa
    AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVWLLGKISGREVAVINFLVGVLSACVAF
    YLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQFLE
    >PAAMIR_3_ORF1  Translation of PAAMIR in frame 3, ORF 1, threshold 1, 429aa
    YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE
    TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV
    RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI
    RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA
    RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY
    FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY

      [Part of this file has been deleted for brevity]

    SEPMNTTRSP
    >PAAMIR_5_ORF11  Translation of PAAMIR in frame 5, ORF 11, threshold 1, 19aa
    WRIRYAASGALFWFGAGPP
    >PAAMIR_5_ORF12  Translation of PAAMIR in frame 5, ORF 12, threshold 1, 10aa
    TMFGEYSKPS
    >PAAMIR_5_ORF13  Translation of PAAMIR in frame 5, ORF 13, threshold 1, 3aa
    GVG
    >PAAMIR_5_ORF14  Translation of PAAMIR in frame 5, ORF 14, threshold 1, 20aa
    QSSASARSTTGITALRVCDM
    >PAAMIR_5_ORF15  Translation of PAAMIR in frame 5, ORF 15, threshold 1, 19aa
    QPTRNRTPRLRMKSSAHSR
    >PAAMIR_5_ORF16  Translation of PAAMIR in frame 5, ORF 16, threshold 1, 107aa
    RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVTPVSENSRPISGRSWCD
    PIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQRYX
    >PAAMIR_6_ORF1  Translation of PAAMIR in frame 6, ORF 1, threshold 1, 11aa
    RGTGWRPPTDR
    >PAAMIR_6_ORF2  Translation of PAAMIR in frame 6, ORF 2, threshold 1, 36aa
    KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS
    >PAAMIR_6_ORF3  Translation of PAAMIR in frame 6, ORF 3, threshold 1, 7aa
    SPPPPDR
    >PAAMIR_6_ORF4  Translation of PAAMIR in frame 6, ORF 4, threshold 1, 8aa
    SCPATRRH
    >PAAMIR_6_ORF5  Translation of PAAMIR in frame 6, ORF 5, threshold 1, 14aa
    ETAPRQRTAEPVPA
    >PAAMIR_6_ORF6  Translation of PAAMIR in frame 6, ORF 6, threshold 1, 61aa
    RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLPATGAGAPRARPSHGAASATPWP
    G
    >PAAMIR_6_ORF7  Translation of PAAMIR in frame 6, ORF 7, threshold 1, 23aa
    SGPGRRCGPGAARSSASASPFPR
    >PAAMIR_6_ORF8  Translation of PAAMIR in frame 6, ORF 8, threshold 1, 18aa
    CAAPIPAQAAPGGHRAAG
    >PAAMIR_6_ORF9  Translation of PAAMIR in frame 6, ORF 9, threshold 1, 8aa
    SRRGTPAR
    >PAAMIR_6_ORF10  Translation of PAAMIR in frame 6, ORF 10, threshold 1, 16aa
    SARAPRGFRTPPAPPG
    >PAAMIR_6_ORF11  Translation of PAAMIR in frame 6, ORF 11, threshold 1, 22aa
    CAESRRRAAQRSRRGGHSGKCW
    >PAAMIR_6_ORF12  Translation of PAAMIR in frame 6, ORF 12, threshold 1, 32aa
    RPRPPARRRLPAAASTGAPNNRCGSAARPGRR
    >PAAMIR_6_ORF13  Translation of PAAMIR in frame 6, ORF 13, threshold 1, 5aa
    PPPAG
    >PAAMIR_6_ORF14  Translation of PAAMIR in frame 6, ORF 14, threshold 1, 407aa
    GPAPATRAGCRAASWRSWERSPAHAGGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFR
    DARRQAAVVVLALHPDRPLWRVDVDVVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGG
    DGRVLREETMAGLDEGPAGGRIDAGEVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAV
    AVATGDGAIQLGGAGAHHGGEDHVGARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQ
    VAHHMVAFPRIDVVRADEHHPLAVVANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVA
    EQRVGALDHRHHRLARVRHVAAHEEPYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADA
    ALAVQLLDREQCAIRVRALDIGGDAGFGEQQADQRPLLVRSHPFPLL
    >PAAMIR_6_ORF15  Translation of PAAMIR 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

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
backtranseq | Back translate a protein 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 MAR/SAR sites in nucleic sequences
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
plotorf | Plot potential open reading frames
prettyplot | Displays aligned sequences, with colouring and boxing
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
seealso | Finds programs sharing group names
showalign | Displays a multiple sequence alignment
showdb | Displays information on the currently available databases
showfeat | Show features of a sequence
showorf | Pretty output of DNA translations
showseq | Display a sequence with features, translation etc
syco | Synonymous codon usage Gribskov statistic plot
tcode | Fickett TESTCODE statistic to identify protein-coding DNA
textsearch | Search sequence documentation text. SRS and Entrez are faster!
transeq | Translate nucleic acid sequences
wobble | Wobble base plot

## 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