EMBOSS: sixpack manual

sixpack

Wiki

The master copies of EMBOSS documentation are available at 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 output sequence file.

Usage

Here is a sample session with sixpack


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

Go to the input files for this example
Go to the output files for this example

Command line arguments

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

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-sequence]
(Parameter 1)

sequence

Nucleotide sequence filename and optional format, or reference (input USA)

Readable sequence

Required

[-outfile]
(Parameter 2)

outfile

Output file name

Output file

<*>.sixpack

-outseq

seqoutall

ORF sequence output

Writeable sequence(s)

<*>.format

Additional (Optional) qualifiers

-table

list

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)

-[no]firstorf

boolean

Count the beginning of a sequence as a possible ORF, even if it is inferior to the minimal ORF size.

Boolean value Yes/No

Yes

-[no]lastorf

boolean

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.

Boolean value Yes/No

Yes

-mstart

boolean

Displays only ORFs starting with an M.

Boolean value Yes/No

Advanced (Unprompted) qualifiers

-[no]reverse

boolean

Display also the translation of the DNA sequence in the 3 reverse frames

Boolean value Yes/No

Yes

-orfminsize

integer

Minimum protein size of Open Reading Frames (ORFs) to display in the translations.

Integer 1 or more

-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

Sequence range

If this is left blank, then the sequence case is left alone.

-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 specified as '@filename'.

Sequence range

full sequence

-[no]number

boolean

Number the sequence at the beginning and the end of each line.

Boolean value Yes/No

Yes

-width

integer

Number of nucleotides displayed on each line

Integer 1 or more

-length

integer

Line length of page (0 for indefinite)

Integer 0 or more

-margin

integer

Margin around sequence for numbering.

Integer 0 or more

-[no]name

boolean

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

boolean

Set this to be false if you do not wish to display the description of the sequence.

Boolean value Yes/No

Yes

-offset

integer

Number from which you want the DNA sequence to be numbered.

Any integer value

-html

boolean

Use HTML formatting

Boolean value Yes/No

Associated qualifiers

"-sequence" associated sequence qualifiers

-sbegin1
-sbegin_sequence

integer

Start of the sequence to be used

Any integer value

-send1
-send_sequence

integer

End of the sequence to be used

Any integer value

-sreverse1
-sreverse_sequence

boolean

Reverse (if DNA)

Boolean value Yes/No

-sask1
-sask_sequence

boolean

Ask for begin/end/reverse

Boolean value Yes/No

-snucleotide1
-snucleotide_sequence

boolean

Sequence is nucleotide

Boolean value Yes/No

-sprotein1
-sprotein_sequence

boolean

Sequence is protein

Boolean value Yes/No

-slower1
-slower_sequence

boolean

Make lower case

Boolean value Yes/No

-supper1
-supper_sequence

boolean

Make upper case

Boolean value Yes/No

-scircular1
-scircular_sequence

boolean

Sequence is circular

Boolean value Yes/No

-squick1
-squick_sequence

boolean

Read id and sequence only

Boolean value Yes/No

-sformat1
-sformat_sequence

string

Input sequence format

Any string

-iquery1
-iquery_sequence

string

Input query fields or ID list

Any string

-ioffset1
-ioffset_sequence

integer

Input start position offset

Any integer value

-sdbname1
-sdbname_sequence

string

Database name

Any string

-sid1
-sid_sequence

string

Entryname

Any string

-ufo1
-ufo_sequence

string

UFO features

Any string

-fformat1
-fformat_sequence

string

Features format

Any string

-fopenfile1
-fopenfile_sequence

string

Features file name

Any string

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile

string

Output directory

Any string

"-outseq" associated seqoutall qualifiers

-osformat

string

Output seq format

Any string

-osextension

string

File name extension

Any string

-osname

string

Base file name

Any string

-osdirectory

string

Output directory

Any string

-osdbname

string

Database name to add

Any string

-ossingle

boolean

Separate file for each entry

Boolean value Yes/No

-oufo

string

UFO features

Any string

-offormat

string

Features format

Any string

-ofname

string

Features file name

Any string

-ofdirectory

string

Output directory

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

-warning

boolean

Report warnings

Boolean value Yes/No

-error

boolean

Report errors

Boolean value Yes/No

-fatal

boolean

Report fatal errors

Boolean value Yes/No

-die

boolean

Report dying program messages

Boolean value Yes/No

-version

boolean

Report version number and exit

Boolean value Yes/No

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.

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

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

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:x13776

Output file format

Output files for usage example

File: x13776.sixpack

File: x13776.fasta

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments