
                                  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 ou
tput 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

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 Pseudomona
s
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 cause
s
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       90
0
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       96
0
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      102
0
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      108
0
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      114
0
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      120
0
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      126
0
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      132
0
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      138
0
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      144
0
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      150
0
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      156
0
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      162
0
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      168
0
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      174
0
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      180
0
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      186
0
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      192
0
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      198
0
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      204
0
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      210
0
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      216
0
     cctcgag                                                                216
7
//

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
