                                   sixpack



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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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 output 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 out
put 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

Display a DNA sequence with 6-frame translation and ORFs
Version: EMBOSS:6.6.0.0

   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 is inferior to the
                                  minimal ORF size.
   -[no]lastorf        boolean    [Y] Count the end of a sequence as a
                                  possible ORF, even if it is 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 protein 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 specified 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   sixpack reads a single nucleotide sequence.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  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 INSDC.
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 (amiR) of
RT   Pseudomonas 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 sequence 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 INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   GOA; Q51417.
DR   InterPro; IPR003211; AmiSUreI_transpt.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

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   misc_difference 1281
FT                   /replace="g"
FT                   /note="conflict"
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

   sixpack writes a text report and an ORF sequence file.

   The output is a standard EMBOSS sequence file.

   The results can be output in one of several styles by using the
   command-line qualifier -osformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
   excel, feattable, motif, nametable, regions, seqtable, simple, srs,
   table, tagseq.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  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 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: 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

   The -minorfsize threshold is in amino acid units.

   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 is less than the
   minimal ORF size or (end only) lacking a STOP codon. See the -firstorf
   and -lastorf options.

   Open reading frames can be restricted to start with a start codon using
   the -mstart option. This may eliminate some or all of the final ORFs at
   the end of each frame.

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
   checktrans       Report STOP codons and ORF statistics of a protein
   cirdna           Draw circular map of DNA constructs
   coderet          Extract CDS, mRNA and translations from feature tables
   getorf           Find and extract open reading frames (ORFs)
   iep              Calculate the isoelectric point of proteins
   lindna           Draw linear maps of DNA constructs
   marscan          Find matrix/scaffold recognition (MRS) signatures in DNA
                    sequences
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   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
   showfeat         Display features of a sequence in pretty format
   showorf          Display a nucleotide sequence and translation in pretty format
   showpep          Display protein sequences with features in pretty format
   showseq          Display sequences with features in pretty format
   syco             Draw synonymous codon usage statistic plot for a nucleotide
                    sequence
   tcode            Identify protein-coding regions using Fickett TESTCODE statistic
   transeq          Translate nucleic acid sequences
   wobble           Plot third base position variability in a nucleotide sequence

Author(s)

   Thomas Laurent formerly at:
   Lion Bioscience Ltd, Compass House, 80-82 Newmarket Road, Cambridge,
   CB5 8DZ, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
