                                   transeq



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Function

   Translate nucleic acid sequences

Description

   transeq reads one or more nucleotide sequences and writes the
   corresponding protein sequence translations to file. It can translate
   in any of the 3 forward or three reverse sense frames, or in all three
   forward or reverse frames, or in all six frames. The translation may be
   restricted to specified regions, for example, corresponding to the
   coding regions of your sequences. It can translate using the standard
   ('Universal') genetic code and also with a selection of non-standard
   codes.

Usage

   Here is a sample session with transeq

   To translate a sequence in the first frame (starting at the first base
   and proceeding to the end):


% transeq tembl:x13776 amir.pep
Translate nucleic acid sequences


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

   Example 2

   To translate a sequence in the second frame:


% transeq tembl:x13776 amir.pep -frame=2
Translate nucleic acid sequences


   Go to the output files for this example

   Example 3

   To translate a sequence in the first frame in the reverse sense
   (starting at the last frame 1 codon and proceeding to the start):


% transeq tembl:x13776 amir.pep -frame=-1
Translate nucleic acid sequences


   Go to the output files for this example

   Example 4

   To translate a sequence in all three forward frames:


% transeq tembl:x13776 amir.pep -frame=F
Translate nucleic acid sequences


   Go to the output files for this example

   Example 5

   To translate a sequence in all three reverse frames:


% transeq tembl:x13776 amir.pep -frame=R
Translate nucleic acid sequences


   Go to the output files for this example

   Example 6

   To translate a sequence in all six forward and reverse frames:


% transeq tembl:x13776 amir.pep -frame=6
Translate nucleic acid sequences


   Go to the output files for this example

   Example 7

   To translate a specific set of regions corresponding to a known set of
   coding sequences:


% transeq tembl:x13776 amir.pep -reg=2-45,67-201,328-509
Translate nucleic acid sequences


   Go to the output files for this example

   Example 8

   To translate a mitochondrial sequence using the mammalian mitochondrion
   genetic code table:


% transeq mito.seq mito.pep -table 2
Translate nucleic acid sequences


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

Command line arguments

Translate nucleic acid sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Protein sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers:
   -frame              menu       [1] Frame(s) to translate (Values: 1 (1); 2
                                  (2); 3 (3); F (Forward three frames); -1
                                  (-1); -2 (-2); -3 (-3); R (Reverse three
                                  frames); 6 (All six frames))
   -table              menu       [0] Code to use (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))
   -regions            range      [Whole sequence] Regions to translate.
                                  If this is left blank, then the complete
                                  sequence is translated.
                                  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
                                  Note: you should not try to use this option
                                  with any other frame than the default,
                                  -frame=1
   -trim               boolean    [N] This removes all 'X' and '*' characters
                                  from the right end of the translation. The
                                  trimming process starts at the end and
                                  continues until the next character is not a
                                  'X' or a '*'
   -clean              boolean    [N] This changes all STOP codon positions
                                  from the '*' character to 'X' (an unknown
                                  residue). This is useful because some
                                  programs will not accept protein sequences
                                  with '*' characters in them.

   Advanced (Unprompted) qualifiers:
   -alternative        boolean    [N] The default definition of frame '-1' is
                                  the reverse-complement of the set of codons
                                  used in frame 1. (Frame -2 is the set of
                                  codons used by frame 2, similarly frames -3
                                  and 3). This is a common standard, used by
                                  the Staden package and other programs. If
                                  you prefer to define frame '-1' as using the
                                  set of codons starting with the last codon
                                  of the sequence, then set this to be true.
   -[no]methionine     boolean    [Y] START codons at the beginning of protein
                                  products will usually code for Methionine,
                                  despite what the codon will code for when it
                                  is internal to a protein. This qualifier
                                  sets all such START codons to code for
                                  Methionine by default.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each 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

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       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

   transeq reads one or more nucleotide sequences.

   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
//

  Input files for usage example 8

  File: mito.seq

>gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete genom
e
GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGCT
TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATTT
GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAAC
TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGACA
GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACATG
AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAGC
CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATCC
CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCTC
GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTTA
AGGGTTGGTAAACTTCGTGCCAGCCACCGCGGTCATACGATCGACCCAAATTAATAGAAGCACGGCGTAAAGAGTGTTAA
GGAGCCACATGAAATAAAGTCAAACCTTAATTAAGCTGTAAAAAGCCCTAATTAAAATTAAGCCAAACTACGAAAGTGAC
TTTAATATAATCTGATCACACGACAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGTCGTAAACCCCAAT
AGTCACAAAACAAGACTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTTGGCGGTGCCTCATACCCA
TCTAGAGGAGCCTGTTCTGTAACCGATAAACCCCGATCAACCTCACCAACCCTTGCTACTTCAGTCTATATACCGCCATC
TTCAGCAAACCCTAAAGGGAGAAAAGTAAGCATAACCATCCTACATAAAAACGTTAGGTCAAGGTGTAACCCATGGGTTG
GGAAGTAATGGGCTACATTTTCTAAGCTAAGAACATCCCCTATACTCACACGAAAGTTTTTATGAAACTTAAAAACTAAA
GGAGGATTTAGTAGTAAATCAAGAGCAGAGTGCTTGATTGAATAAGGCCATGAGGGCACGCACACACCGCCCGTCACCCT
CCTCAAGTACCCCAGCTATAAACCCCAGTTCGTTAACTCAGGCCAAGCAATTATACGAGAGGAGACAAGTCGTAACAAGG
TAAGCATACCGGAAGGTGTGCTTGGACAAAACAAGATATAGCTTAAACAAAGCATGTAGTTTACACCTAGAAGATTCCAC
AGCCCGTGTATATCTTGAACTAGCCCTAGCCCACACCCTCCCCACCTCTACTACCACAAATCAATCAAATAAAACATTTA
CCATCCCTTCAAAGTATAGGAGATAGAAATTTAAATATCAGTGGCGCTATAGAGATAGTACCGTAAGGAAAGATGAAAGA
AAAACCTAAAAGTAATAAAAAGCAAAGCTTACCACTTGTACCTTTTGCATAATGACTTAACTAGTAATAAATTAGCAAAG
AGACCTTAAGTTAAATTACCCGAAACCAGACGAGCTACTTATGAGCAGCACCTAGAACGAACTCATCTATGTGGCAAAAT
AGTGAGAAGACTTATAAGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTGTCCCTGAAAAGAATCTCAGTTC
AACATTAAATAATACTAAAAGCCCATGCCAAGCCTTAACGTATATTTAACTGTTAATCTAAAAAGGTACAGCTTTTTAGA
AATGGGTACAACCTTGACTAGAGAGTAAAATCAAACATAAACATAGTTGGCCTAAAAGCAGCCATCAATTAAGAAAGCGT
TCAAGCTCGACAACAAAATAATGTTTTAATTCCAACATTAAGTAAATCAACTCCTAGCCTGACTATTGGACTAATCTATA
CAAATATAGAAGCAATACTGTTAATATGAGTAACAAGAAATTTTTCTCCTAGCACAAGCTTACACCAGTAACTGATAATA
TACTGATAATTAACAGCAAATAAATAAAACCCAACACTAAATTATTTATTAAAATACTGTTAACCCAACACAGGCGTGCA
TTAAGGAAAGATTAAAAAAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCAT
AACCAGTATTAGAGCACTGCCTGCCCGGTGACTAATCGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAAT
CACTTGTTCTCTAATTAGGGACTTGTATGAATGGCCACACGAGGGTTTTACTGTCTCTTACTTTTAATCAGTGAAATTGA
CCTCTCCGTGAAGAGGCGGAGATAACAAAATAAGACGAGAAGACCCTATGGAGCTTCAATTAATCAACCCAAAAACCATA
ACCTTAAACCACCAAGGGATAACAAAACCTTATATGGGCTGACAATTTCGGTTGGGGTGACCTCGGAGTACAAAAAACCC
TCCGAGTGATTAAAACTTAGGCCCACTAGCCAAAGTACAATATCACTTATTGATCCAATCCTTTGATCAACGGAACAAGT
TACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGATCAGGAC
ATCCTAATGGTGCAGCTGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTA
ATCCAGGTCGGTTTCTATCTATTACGCATTTCTCCCAGTACGAAAGGACAAGAGAAATAAGGCCAACTTCAAACAAGCGC
CTTCAAACAATTAATGACCTAGTCTCAACTTAATAATTAAGCGCAAACAAACCTGCCCAAGACCAGGGCCTTGTTGAGGT
GGCAGAGTTCGGTAATTGCATAAAACTTAAACTTTTACACCCAGAGGTTCAAATCCTCTCCCCAACAAAATGTTTATAAT
TAACATTCTAACACTCATTCTCCCCATCCTCCTAGCCGTAGCATTCCTAACGCTAGTAGAACGCAAAATTCTAGGCTATA
TGCAGTTCCGAAAGGGGCCAAACATCGTAGGCCCACATGGCTTACTCCAACCCTTTGCCGATGCAATTAAATTATTCACT
AAAGAACCCCTACGGCCAGCTACATCCTCAACTACTATGTTTATCATTGCACCAGTACTAGCCCTAACCCTGGCCCTCAC
TATATGAAGCCCCCTACCCATACCATACCCCCTCATTAACATAAACCTAGGAGTATTATTCATATTAGCAATATCCAGCC
TAGCCGTCTACTCCATCCTATGATCAGGCTGAGCCTCCAACTCAAAATACGCACTAATTGGAGCCCTACGAGCAGTAGCA
CAAACAATCTCATATGAGGTAACACTAGCCATTATCCTCCTATCAGTACTCCTAATAAACGGCTCCTACACCTTATCAAC
ATTAGCCACAACACAAGAACAACTATGATTACTATTCCCATCATGACCCTTAGCCATAATGTGATTCATCTCCACCCTAG
CAGAAACTAATCGAGCTCCTTTTGATCTAACAGAGGGAGAATCAGAACTCGTATCAGGCTTCAACGTAGAATATGCAGCA
GGCCCTTTCGCCCTATTCTTCCTGGCAGAATACGCCAACATCATTATAATGAATATACTCACAGCCATTTTATTCCTAGG


  [Part of this file has been deleted for brevity]

CATTGTCTTCTGCGCCTTCATCACTAGTCTAGTTCCCGCAATAGTATATCTTCACACAAACCAAGAAACACTCATCTCAA
ACTGACACTGAATCACAATCCAAACCCTCAAACTAACACTTAGCTTTAAAATAGATTACTTTTCACTTATATTTATACCA
GTAGCACTATTCATTACATGATCCATCATAGAATTCTCAATATGATATATGCACTCCGACCCCTACATCAACCAATTTTT
TAAATACTTACTCCTCTTCCTCATCACCATACTAATCCTTGTTACAGCTAACAATCTCTTCCAACTTTTCATCGGATGAG
AAGGAGTAGGAATTATATCCTTCTTACTAATTGGCTGATGATTCGGACGAACAGATGCAAATACAGCCGCCCTCCAAGCA
ATCCTATACAATCGTATCGGAGACATTGGACTCCTTGCATCAATAGCATGATTTCTCTCTAATATAAACACATGAGACCT
AGAACAAATCTTTATACTCAACCAAAACCCCTTAAATTTCCCCCTCATAGGACTCGTACTAGCCGCAGCAGGAAAATCGG
CTCAATTCGGACTCCACCCTTGACTCCCATCAGCAATAGAAGGTCCTACCCCAGTCTCAGCCCTACTCCACTCAAGCACA
ATAGTTGTAGCAGGAATCTTCTTGCTTGTCCGCTTCTACCCATTAATAGAAAATAACAAGCTAATCCAAACAGTAACCCT
CTGCTTAGGCGCTATCACAACTCTATTTACAGCCATCTGTGCCCTCACCCAAAACGACATCAAAAAAATTATTGCTTTCT
CCACCTCCAGCCAGCTAGGCCTAATAATAGTAACAATCGGCCTTAACCAACCTTACCTAGCATTCCTACACATTTGCACA
CACGCCTTCTTTAAAGCTATACTATTCCTATGTTCTGGCTCCATCATCCATAACCTAAACAACGAACAAGATATCCGAAA
AATAGGAGGGCTATTTAAGGCCCTCCCATTCACCACAACCGCCCTTATCATCGGATGTCTTGCACTAACAGGAATGCCAT
TCCTGACCGGATTCTACTCCAAAGATCCCATTATTGAAGCCGCCACTTCGTCTTATACCAACGCCTGAGCCCTATTACTG
ACCTTAATCGCCACCTCCCTTACGGCCGTCTATAGCACCCGCATCATTTTCTTTGCACTACTAGGACAACCCCGCTTCCC
TCCCTCCACAACCATTAACGAAAATAATCCACTGTTAATCAACCCTATCAAACGACTACTCGTCGGAAGTATCTTCGCTG
GCTTCATCCTATCCAACAGTATTCCCCCAATAACTACACCTTTAATAACCATACCCCTGCACTTAAAATTAACCGCCCTT
GCAATAACAACCCTAGGCTTCATCATCGCATTCGAAATTAACCTTGACACACAAAATCTAAAGCACAAGCACCCATCAAA
CTCCTTTAAATTCTCCACCTTACTAGGTTATTTCCCCACAATCATACATCGCCTACCCCCTCACCTTGACCTGTTAATAA
GCCAAAAACTAGCAACTTCCCTACTAGATCTAACTTGACTAGAAACTATTTTACCAAAAACCACAGCCCTTATCCAACTA
AAAGCCTCTACACTAACCTCTAACCAACAAGGCCTCATCAAACTCTACTTCTTATCTTTCCTCATCACCATCACCCTCAG
CATAATCTTATTTAACTACCCCGAGTAATCTCCATAATAATTACAACACTAATAAATAAAGACCAACCCGTAACAATCAC
CAACCAAACACCATAACTATATAATGCCGCAATCCCTGTAGCCTCCTCACTAAAAACCCCAGAACCCCCAGTATCATAAA
CAACCCAGTCCCCTAGTCCATCAAACTCAAACATAATCTTCACCTCCCCACTCTTCAAAGCATAAATCACAATTAAAAAC
TCCACCACCAACCCTAAAACAAATGCTCCTAGTACAACTTTATTAGAAACCCAAACCTCAGGATACTGTTCAGTAGCCAT
AGCTGTTGTATAACCAAATACTACCAGCATTCCCCCCAAATAAATCAAAAACACCATTAACCCCAAAAACGAACCACCAA
AACTCAAAATAACTCCACATCCAACACCACCACCCACAATCAACCCTAAACCCCCATAAATAGGTGAAGGCTTTGAAGAA
ACCCCCACAAAACTAATTACAAAAATAATACTTAAAATGAAAACAATATACATTATCATTATTCTCACATGGACTTCAAC
CATGACCAATGACATGAAAAATCATCGTTGTTATTCAACTACAAGAACACCAATGACCAACATCCGAAAAACACACCCAC
TAATAAAAATCGTCAACGACGCATTCGTCGATCTCCCCACCCCATCAAATATCTCTTCATGATGGAACTTCGGCTCCCTA
CTCGGCCTCTGCTTAATTATACAAATCCTAACAGGCCTATTCCTAGCAATACACTACACACCAGACACAACAACCGCCTT
CTCATCAGTCACACACATCTGCCGAGACGTGAATTACGGCTGAATTATCCGATACCTACATGCAAATGGGGCTTCTATAT
TCTTCATCTGCCTCTACGCTCACATAGGACGAGGCCTATACTACGGCTCCTACGCCTTCCGAGAAACATGAAATATTGGA
GTTATTCTACTATTCACAGTTATAGCCACCGCATTCGTAGGCTACGTCCTGCCCTGAGGACAAATATCATTCTGAGGCGC
AACTGTAATCACTAACCTCCTATCAGCAATCCCATACATTGGTACCACCCTAGTCGAATGAATCTGAGGCGGTTTCTCTG
TAGATAAAGCAACACTAACACGCTTTTTTGCCTTTCACTTTATCCTCCCCTTCATCATCCTAGCATTAGCAATTGTCCAC
CTTATTTTCCTTCACGAAACAGGATCCAACAACCCCACAGGCATCCCATCCGACATAGATAAAATCCCATTCCACCCCTA
CCACACAATTAAAGACATTCTAGGTGCCCTATTACTAATCCTAATCCTACTAATACTAACCCTATTCGCACCCGACCTAC
TTGGAGACCCAGACAACTATACCCCAGCAAACCCACTCAGTACCCCAGCACACATTAAACCAGAATGGTATTTTCTATTC
GCATACGCAATCCTACGATCAATCCCCAACAAACTAGGCGGAGTCTTAGCCCTACTACTCTCAATCCTAATCCTAGCCTT
CATCCCAATACTCCACACATCCAATCAACGAAGCATAATATTTCGACCCTTTAGCCAGTTCTTGTTCTGAGTCCTAGTCG
CAGATCTACTAACCCTAACATGGATCGGCGGCCAACCAGTAGAACACCCCTACATAATTGTAGGCCAACTCGCATCCATC
CTCTATTTCCTCTTAATTCTAGTATTAATACCAGTAACTAGTCTTATCGAGAACAAACTTATAAAATGAAGAGTCTTTGT
AGTATAATTAAATACCCCGGTTTTGTAAACCGGAAAAGGAGACAAGACACACCTCCCTAAGACTCAAGGAAGAAGTATTA
CACTCCACCATCAGCACCCAAAGCTGAAGTTCTACATAAACTATTCCCTGAAAAAGTATATTGTACAATAACCACAGGAC
CACAGTACTATGTCCGTATTGAAAATAACTTGCCTTATTAGATATTATTATGTAACTCGTGCATGCATGTACTTCCACAT
AATTAATAGCGTCTTTCCATGGGTATGAACAGATATACATGCTATGTATAATTGTGCATTCAATTATTTTCACCACGAGC
AGTTGAAGCTCGTATTAAATTTTATTAATTTTACATATTACATAATATGTATTAATAGTACAATAGCGCATGTTCTTATG
CATCCCCAGATCTATTTAAATCAAATGATTCCTATGGCCGCTCCATTAGATCACGAGCTTAGTCAGCATGCCGCGTGAAA
CCAGCAACCCGCTTGGCAGGGATCCCTCTTCTCGCACCGGGCCCATCACTCGTGGGGGTAGCTATTTAATGATCTTTATA
AGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTCGTTCCCCTTAAATAAGACATCTCGATGG

Output file format

   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: amir.pep

>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP
KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG
YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT*
FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR
RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC
TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG
PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR
AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR
CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP
VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL
VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV
PRX

  Output files for usage example 2

  File: amir.pep

>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR
NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG
TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD
SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG
ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL
LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV
RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV
RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV
PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD
AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL
SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW
LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF
LE

  Output files for usage example 3

  File: amir.pep

>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP
SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS
RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR
WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS
TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC
WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR
CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW
RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR
RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS
GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG
TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R
RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS
GT

  Output files for usage example 4

  File: amir.pep

>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP
KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG
YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT*
FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR
RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC
TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG
PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR
AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR
CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP
VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL
VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV
PRX
>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR
NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG
TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD
SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG
ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL
LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV
RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV
RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV
PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD
AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL
SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW
LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF
LE
>X13776_3 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE
TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV
RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI
RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA
RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY
FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY
DIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWS
ASMGGGPLP*APTRCSAACASCRCWSSTRRGRSATPWSCS*SASVVRCASAGRRRKPSTC
RWTWSSPAFSRMATTTRSLRCSPPGLRALPWWRWWSTKAPRCSRRSSSWSATA*SPSRSM
PTGCCLCWYRRGASARKWRS*SRRPSSSRTASPARPGSTRPRCC*CSAMAGTSARRTSTC
RGKR*SGASRS*RSLRSCWETSRPPERSGPTRTITRGVSSSCWDWFCCTLARCCFSMPSG
CWARSAVGRWR*STSWSAC*APASRST*SFPQQPGRAR*RPER*PCYSLLPICGWPPTSS
SX

  Output files for usage example 5

  File: amir.pep

>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP
SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS
RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR
WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS
TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC
WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR
CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW
RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR
RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS
GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG
TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R
RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS
GT
>X13776_5 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
LEELVGGHPQIGKSE*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA
QQPDGIEKQHRANVQQNQSQHDDDTPLVIVLVGPDRSGGRLVSQQLLSDLQDRLAPLHRF
PRQVLVRLALVPAMALHQQHLGLVDPGLAGDAVLELLGLLLQLRHFLADAPRRYQHRQHP
VGIERLGDHAVALQLDDLREHRGAFVLHQRHQGSARSPGGEQRSDLVVVAILENAGEDHV
HRHVEGFRRRPALAHRTTDADQLQDQGVADLPRRVEDQHLQLAQAAEQRVGAHGSGPPPM
LADQSSRLCTTT*GSGRIGSGDCQRTWNTPRASISAMREDRRLWLFWRSTRTGPCGASMS
MSYRCRCTSSTRQLPAACAARPSNKVCQ*AASAQAVMVAFSGKKPWQAWTKARLAGVSML
EK*GATTTCPSATSLSIFATSASLVVRLAIGGRLPSP*RRAMARYSSAVPVPTTVEKTTS
ARAW*MRSTARCKSSSEGYSGM*ISSSTVPPCWRYRWRITWLLSRG*M*SEPMNTTRSP*
WRIRYAASGALFWFGAGPP*TMFGEYSKPS*GVG*QSSASARSTTGITALRVCDM*QPTR
NRTPRLRMKSSAHSR*RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVT
PVSENSRPISGRSWCDPIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQ
RYX
>X13776_6 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
RGTGWRPPTDR*KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS*SPPPPDR*SCP
ATRRH*ETAPRQRTAEPVPA**RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLP
ATGAGAPRARPSHGAASATPWPG*SGPGRRCGPGAARSSASASPFPR*CAAPIPAQAAPG
GHRAAG*SRRGTPAR*SARAPRGFRTPPAPPG*CAESRRRAAQRSRRGGHSGKCW*RPRP
PARRRLPAAASTGAPNNRCGSAARPGRR*PPPAG*GPAPATRAGCRAASWRSWERSPAHA
GGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFRDARRQAAVVVLALHPDRPLWRVDVD
VVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGGDGRVLREETMAGLDEGPAGGRIDAG
EVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAVAVATGDGAIQLGGAGAHHGGEDHVG
ARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQVAHHMVAFPRIDVVRADEHHPLAVV
ANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVAEQRVGALDHRHHRLARVRHVAAHEE
PYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADAALAVQLLDREQCAIRVRALDIGGDA
GFGEQQADQRPLLVRSHPFPLL*LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPA
VP

  Output files for usage example 6

  File: amir.pep

>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP
KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG
YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT*
FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR
RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC
TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG
PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR
AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR
CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP
VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL
VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV
PRX
>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR
NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG
TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD
SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG
ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL
LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV
RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV
RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV
PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD
AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL
SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW
LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF
LE
>X13776_3 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE
TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV
RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI
RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA
RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY
FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY
DIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWS
ASMGGGPLP*APTRCSAACASCRCWSSTRRGRSATPWSCS*SASVVRCASAGRRRKPSTC
RWTWSSPAFSRMATTTRSLRCSPPGLRALPWWRWWSTKAPRCSRRSSSWSATA*SPSRSM
PTGCCLCWYRRGASARKWRS*SRRPSSSRTASPARPGSTRPRCC*CSAMAGTSARRTSTC
RGKR*SGASRS*RSLRSCWETSRPPERSGPTRTITRGVSSSCWDWFCCTLARCCFSMPSG
CWARSAVGRWR*STSWSAC*APASRST*SFPQQPGRAR*RPER*PCYSLLPICGWPPTSS
SX
>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP
SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS
RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR
WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS
TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC
WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR
CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW
RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR
RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS
GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG
TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R
RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS
GT
>X13776_5 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
LEELVGGHPQIGKSE*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA
QQPDGIEKQHRANVQQNQSQHDDDTPLVIVLVGPDRSGGRLVSQQLLSDLQDRLAPLHRF
PRQVLVRLALVPAMALHQQHLGLVDPGLAGDAVLELLGLLLQLRHFLADAPRRYQHRQHP
VGIERLGDHAVALQLDDLREHRGAFVLHQRHQGSARSPGGEQRSDLVVVAILENAGEDHV
HRHVEGFRRRPALAHRTTDADQLQDQGVADLPRRVEDQHLQLAQAAEQRVGAHGSGPPPM
LADQSSRLCTTT*GSGRIGSGDCQRTWNTPRASISAMREDRRLWLFWRSTRTGPCGASMS
MSYRCRCTSSTRQLPAACAARPSNKVCQ*AASAQAVMVAFSGKKPWQAWTKARLAGVSML
EK*GATTTCPSATSLSIFATSASLVVRLAIGGRLPSP*RRAMARYSSAVPVPTTVEKTTS
ARAW*MRSTARCKSSSEGYSGM*ISSSTVPPCWRYRWRITWLLSRG*M*SEPMNTTRSP*
WRIRYAASGALFWFGAGPP*TMFGEYSKPS*GVG*QSSASARSTTGITALRVCDM*QPTR
NRTPRLRMKSSAHSR*RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVT
PVSENSRPISGRSWCDPIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQ
RYX
>X13776_6 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
RGTGWRPPTDR*KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS*SPPPPDR*SCP
ATRRH*ETAPRQRTAEPVPA**RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLP
ATGAGAPRARPSHGAASATPWPG*SGPGRRCGPGAARSSASASPFPR*CAAPIPAQAAPG
GHRAAG*SRRGTPAR*SARAPRGFRTPPAPPG*CAESRRRAAQRSRRGGHSGKCW*RPRP
PARRRLPAAASTGAPNNRCGSAARPGRR*PPPAG*GPAPATRAGCRAASWRSWERSPAHA
GGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFRDARRQAAVVVLALHPDRPLWRVDVD
VVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGGDGRVLREETMAGLDEGPAGGRIDAG
EVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAVAVATGDGAIQLGGAGAHHGGEDHVG
ARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQVAHHMVAFPRIDVVRADEHHPLAVV
ANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVAEQRVGALDHRHHRLARVRHVAAHEE
PYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADAALAVQLLDREQCAIRVRALDIGGDA
GFGEQQADQRPLLVRSHPFPLL*LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPA
VP

  Output files for usage example 7

  File: amir.pep

>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
VPLAEHLLDHHQPGEASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLRNRRHRRY
VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE
X

  Output files for usage example 8

  File: mito.pep

>NC_001321.1_1 Balaenoptera physalus mitochondrion, complete genome
VNY*SAHDHNMTEVSYIWYFFIFFGGLARTPLWP**VSSQSDKL*LGLDVFVIWLAQPTC
AVKLMVTGHSTPLFPPGSKNCMS**TKPPSFHTMLTLCLDIHHPP*QARP*I*KPFYL*I
NTKSDTSPMMKMHERHPYPMRWCSLNTYKA*HWKCLDGSSQPHWH**FGPSLSISS*QTY
TCKYPHPSENAL*IMKIK*SGYQAR*H*QLTTPRLATPPRDTAVMKIKL*TKVRLSHVNL
*VGKLRASHRGHTIDPN**KHGVKSVKEPHEMKSNLN*AVKSPN*N*AKLRKWL*YNLIT
RQL*SKLGLDTPLCLVVNPNSHKT*LFA*VLLATA*NSKDLAVPHTHLEEPVL*PMNPDQ
PHQPLLLQSMYRHLQQTLKGEK*A*PSYMKTLGQGVTHGLGSNGLHFLS*EHPLYSHESF
YET*KLKEDLVVNQEQSAWLNKAM*ARTHRPSPSSSTPAMNPSSLTQAKQLYE**QVVT*
*AYRKVCLDKT*YSLNKACSLHLEDSTARVYLELALAHTLPTSTTTNQSNKTFTIPSKY*
**KFKYQWRY*DSTV*KDE*KT*K**KAKLTTCTFCMMT*LVMN*Q*DLKLNYPKPDELL
MSST*NELIYVAK*WEDL*VEVKSLTSLVMAGCPWKESQFNIK*Y*KPMPSLNVYLTVNL
K*YSFLEMGTTLT*E*NQT*T*LA*KQPSIKKAFKLDNKMMF*FQH*VNQLLAWLLD*SM
QM*KQYC*YE*QEIFLLAQAYTSNW*YTDN*QQMNKTQH*IIY*NTVNPTQACIKE*LKK
VKGTRQTQTPPVYQKHHL*HNQY*STACPVTNR*TAAVSWPCKGSMITCSLI*DLYEWPH
EGFTVSYF*SVKLTSPW*GGDNKM*REDPMELQLINPKTMTLNHQGMTKPYMGWQFRLGW
PRSTKNPPSD*NLGPLAKVQYHLLIQSFDQRNKLP*G*QRNPILESMSTMGFTTSMLDQD
ILMVQLLL*VRLFND*SPTWSEF*PE*S*SVSIYYAFLPVRKDK*NKANFKQAPSNN*WP
SLNLMIKRKQTCP*PGPCWGG*VR*LHKT*TFTP*GSNPLPNKMFMINILTLILPILLAV
AFLTLVERKILGYMQFRKGPNIVGPHGLLQPFADAIKLFTKEPLRPATSSTTMFIIAPVL
ALTLALTMWSPLPMPYPLINMNLGVLFMLAMSSLAVYSILWSGWASNSKYALIGALRAVA
QTISYEVTLAIILLSVLLMNGSYTLSTLATTQEQLWLLFPSWPLAMMWFISTLAETNRAP
FDLTEGESELVSGFNVEYAAGPFALFFLAEYANIIMMNMLTAILFLGTFHNPHNPELYTA
NLIIKTLLLTMSFLWIRASYPRFRYDQLMHLLWKNFLPLTLALCMWHISLPIMTASIPPQ
T*EMCLMKELLW*SK***PKSSYF*NN*NRTYP*EFKVLRATMLHYNLQ*GQLNKLSGPY
PENVGSYPSHTNKPINPYYPPDNPYP*YNNGSHQLSLTISLNWLRNEHNSLHPYHNKKSY
SPGH*SFYQVPPNTSHCFRTPHNSSHH*LNAL*PMNYYKTI*PNSIHTHNSSPSHQTGIS
PLPLLSS*SNT*YPPNH*PNPINMTKTSSLINPMPNFTIN*PTPNINHILTFHLN**L*W
TKPNTTSKNHSLLINCPH*MNNGHSTM*SNPNITKSTNLHHNNLHHIYIIYPKLNYHYIV
TVSNLK*NTRHHNPYHTHFTLD**TPTTIGVYTQMNNYS*TNKKWYTHCTNIHSHYSITQ
PMLLYTSYLLHSTNTISLHK*YKNKMTIQLHKTNSSPTNSNRNFHYATTPHTNTLNPTMG
V*VKP*P*AFKALSKYNLLNSCPM*TA*LYLTSIECKSNALIKLNPH*IGGMHLPRIFS*
QLNTLINWLQSTSPAA*KK*REKSRQDLKLLPWICNSKWSFTTGLGKK*TQPLSLDLQSN
TYSAILPMFMNRWLFSTNHKDIGTLYLLFGAWAGMVGTGLSLLIRAELGQPGTLIGDDQV
YNVLVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLM
ASSMIEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKP
PAMTQYQTPLFVWSVLVTAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQH
LFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMVSIGFLGFIVWAHHMF
TVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPALMWALGFIFLFTVGGL
TGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNTTWAKIH
FMIMFVGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNTISSMGSFISLTAVMLMIFIIW
EAFTSKREVLAVDLTSTNLEWLNGCPPPYHTFEEPAFVNPKWS*KEGIEPSPIGFKPTS*
LLCLSL*T*Y**NLM*LCQS*VTSENPVYLHGMSIPT*FP*CSITHH**APTLSRSYTNN
RFSN*LFSSLHYYPNAYNQINTY*YN*RP*S*NCLNYPPSHYLNFNCLAFITDPLHN*RS
Q*PLPHCKNN*SPMMLKLWVYRLR*PKLRLLYNPNI*PKA**TTII*S**PSCLTY*NNN
PNISLI**RTPLMGRTLLGPKN*CNP*TPKPNNLNINTT*PILWTML*DLRLKPQFHTNC
P*TSTP*SLWKMICINTMTSL*S*ISINLLS**L*VYNSP*WYATI*YINMTPYYSINTL
NPLCIIPIKNLKALLFP*PQTSTYQNTKTTSSLKHHMNENLFAPFMIPVMLGIPITTLII
ILPSMLFPAPNRLINNRTIAIQQWLTKLTSKQLMNVHSPKGQTWSLMLISLFLFIASTNL
LGMLPHSFTPTTQLSMNVGMAIPLWAGTVTTGFRNKTKMSLAHLLPQGTPTFLIPMLVII
ETISLFIQPVAWAVRLTANITAGHLLMHLIGETTLALMNINLFSAFITFTILALLTILEF
AVALIQAYVFTLLVSLYLHDNT*WPTKPTHTT**TPALDPSPELYQPF**HQA*LYDFTS
TQYSY*L*ACQQMF*QYTNDGEMSSEKAPSKAIMHQPSK*AYDTE*FYLSSQKSYFSQAS
SEPSTTQALPLLQN*ADVDHQQASAL*IP*KFPFSTPPYY*PLAYLLPEPTMAW*KETAN
TYFKHSSSQLH*ASTSPYYKHQSTTKPLSQSQTESTAPPSL*PQAFMGYM*SLDLLSLSS
VSYVK*NSTSHQTTTLALNVPLDTDIS*TSYDYFFMYLSIDEVPSPFSINKYNWLPIS*F
RCTPKKNNKPSTNTTNKYNTSPTTRIHRLLTSTTKRMR*KNKPMWMRIWPH*ISPPTLLH
KILLGGHYFPSLWL*NRSLTPPSLSNSVKQPKHNTHNSLILNLPTSSQPSLWMNS**P*M
SWMWYLV*DKTSDFDPLDCDQIHNYQMTLIHMNILMAFSMSLMGLLMYRSHLMSALLCLE
GMMLSLFVLAALTILSSHFTLANMMPIILLVFAACEAAIGLALLVMVSNTYGTDYVQNLN
LLQC*NLLFLQSY*YP*PDYQKMT*SELTPQPTVY*LASQAFSSSINSTTTALTTH*YSS
PTPFLPHSWS*QYDSFP*Y**QVNPISSKNHQSEKNSTLRY*SHYKPS*L*HLLPLN*SY
FMSYLKPH*SLPLSLSLAGATKQNDSMPDYTSYSMH*LDLSHY**H*YIYKMQQDP*TFY
SYNTELNHYLRPDPTSSYD*PA**PS**KYLSMDYTFDCPKHT*KPPLQAP*SLQPYY*N
LEAMAYYELHPYSIP*QNT*HTHFLYSLFEE*S*PALSVYVKQT*NH*LHIPQLVT*HSS
SQLSSSKPPEAM*GPLP**LPTASHPPYYSVWQTRTTNAFMAEP*FCPEAYKSFYH**PV
DDY*QA*QILHYPQPST*SENYS*SCRSSHDQIPLFS**EQML*LLLSTLYMY*S*HNVA
NTHTTSMMSPLPSHESMP**PYTLFPSCSYH*TLKSS*ALSTVSMV*K*R*FVKLTMEDQ
NFLLTEKVLQELLIHAPTPNSCGFFKLLQDSSYPLVLGAKKLVQLQMKVMNLFTSFTLLT
LLILTTPIMMSHTGSHVNNKYQSYVKNIVFCAFITSLVPAMVYLHTNQETLISNWHWITI
QTLKLTLSFKMDYFSLMFMPVALFITWSIMEFSMWYMHSDPYINQFFKYLLLFLITMLIL
VTANNLFQLFIGWEGVGIMSFLLIGWWFGRTDANTAALQAILYNRIGDIGLLASMAWFLS
NMNTWDLEQIFMLNQNPLNFPLMGLVLAAAGKSAQFGLHPWLPSAMEGPTPVSALLHSST
MVVAGIFLLVRFYPLMENNKLIQTVTLCLGAITTLFTAICALTQNDIKKIIAFSTSSQLG
LMMVTIGLNQPYLAFLHICTHAFFKAMLFLCSGSIIHNLNNEQDIRKMGGLFKALPFTTT
ALIIGCLALTGMPFLTGFYSKDPIIEAATSSYTNAWALLLTLIATSLTAVYSTRIIFFAL
LGQPRFPPSTTINENNPLLINPIKRLLVGSIFAGFILSNSIPPMTTPLMTMPLHLKLTAL
AMTTLGFIIAFEINLDTQNLKHKHPSNSFKFSTLLGYFPTIMHRLPPHLDLLMSQKLATS
LLDLTWLETILPKTTALIQLKASTLTSNQQGLIKLYFLSFLITITLSMILFNYPE*SP**
LQH**MKTNP*QSPTKHHNYMMPQSL*PPH*KPQNPQYHKQPSPLVHQTQT*SSPPHSSK
HKSQLKTPPPTLKQMLLVQLY*KPKPQDTVQ*P*LLYNQMLPAFPPNKSKTPLTPKTNHQ
NSK*LHIQHHHPQSTLNPHK*VKALKKPPQN*LQK*YLKWKQYTLSLFSHGLQPWPMTWK
IIVVIQLQEHQWPTSEKHTH**KSSTTHSSISPPHQMSLHDGTSAPYSASA*LYKS*QAY
S*QYTTHQTQQPPSHQSHTSAETWITAELSDTYMQMGLLYSSSASTLT*DEAYTTAPTPS
EKHEMLELFYYSQL*PPHS*ATSCPEDKYHSEAQL*SLTSYQQSHTLVPP*SNESEAVSL
*MKQH*HAFLPFTLSSPSSS*H*QLSTLFSFTKQDPTTPQASHPT*MKSHSTPTTQLKTF
*VPYY*S*SY*Y*PYSHPTYLETQTTMPQQTHSVPQHTLNQNGIFYSHTQSYDQSPTN*A
ES*PYYSQS*S*PSSQYSTHPINEA*YFDPLASSCSES*SQIY*P*HGSAANQ*NTPT*L
*ANSHPSSISS*F*Y*YQ*LVLS*TNL*NEESL*YN*MPRFCKPEKET*HTSL*LKEEVL
HSTISTQSWSST*TIPWKSMLYNNH*TTVLCPYWK*LALLDIIM*LVHACTST*LMASFH
GYEQMYMLCMIVHSIIFTTSSWSSY*ILLILHIT*YVLMVQ*RMFLCIP*SI*IKWFLWP
LH*ITSLVSMPRETSNPLG*DPSSRTGPITRGGSYLMIFM*HLVLTSGPY*LKIAHSFPL
NKTSRW

   One or more peptide sequences are written out.

   The names of the resulting protein sequences are formed from the name
   of the input nucleic acid sequence with '_' and the translation frame
   appended to it. Thus a nucleic acid sequence with the name 'XYZ'
   franslated in all 6 frame would produce protein sequences with the
   names: 'XYZ_1', 'XYZ_2', 'XYZ_3', 'XYZ_4', 'XYZ_5', 'XYZ_6'.

   If regions are specified, they are taken to be translated in frame 1
   and so the output name would be 'XYZ_1'.

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 EMBOSS REBASE restriction enzyme data files are stored in directory
   'data/REBASE/*' under the EMBOSS installation directory.

   These files must first be set up using the program 'rebaseextract'.
   Running 'rebaseextract' may be the job of your system manager.

   The data files are stored in the REBASE directory of the standard
   EMBOSS data directory. The names are:
     * embossre.enz Cleavage information
     * embossre.ref Reference/methylation information
     * embossre.sup Supplier information

   The column information is described at the top of the data files

   The reported enzyme from any one group of isoschizomers (the prototype)
   is specified in the REBASE database and the information is held in the
   data file 'embossre.equ'. You may edit this file to set your own
   preferred prototype, if you wish.

   The format of the file "embossre.equ" is
   Enzyme-name Prototype-name

   i.e. two columns of enzyme names separated by a space. The first name
   of the pair of enzymes is the name that is not preferred and the second
   is the preferred (prototype) name.

Notes

   Termination (STOP) codons are translated as the character *. The -trim
   option removes all all X and * characters from the right end of the
   translation. This trimming process starts at the end and continues
   until the next character is not an X or a *. The -clean option changes
   all STOP codon positions from the * character to X (an unknown
   residue). This is useful because some programs will not accept protein
   sequences with * characters in them.

   The reverse frame '-1' is defined as the translation you get when you
   use the reverse-complement of the sequence with the same codon phase as
   the codon in frame '1'. Thus the sequence ACTGG in frame 1 is the
   translation of the codons ACT,GG; the translation of frame -1 uses
   these same codons, reverse complemented: forward sense ACT GG reverse
   sense TGA CC reverse-complement CC AGT frame -1 translation S

   Frame -1 is the translation of CCAGT (the reverse complement of ACTGG)
   using the codon AGT (the first bases CC are ignored). The result is the
   peptide S.

   Similarly frame -2 is the phase used by frame 2, CAG T (the first base
   C is ignored). The last base cannot be successfully translated and is
   output as the unknown residue X. The result is the peptide QX.

   Frame -3 is the phase used by frame 3, CCA GT. The last two bases will
   translate to V as it does not matter what the next base is. (GTA, GTC,
   GTG, GTT all code for V). The result is the peptide PV.

   The alternative way of generating the reverse translation frames used
   by some people is that frame -1 is made by taking the frame '1' of the
   reverse complement. There is no correspondence between the codons used
   in frame 1 and -1, 2 and -2, 3 and -3; the codons used change with the
   length modulus 3.

   There does not appear to be a convention on which definition to use.
   The Staden package uses the same convention as this program. The GCG
   package sneakily avoids the problem by naming the frames using letters
   (a, b, c, d, e, f). If you really need to define frame -1 as the frame
   given when you reverse complement the sequence and then start
   translating at the first frame in the resulting sequence, then use the
   -alternative qualifier.

References

   None.

Warnings

   When translating using a non-standard genetic code, you should check
   the table carefully for deviations from your particular organism's
   code.

   When using the -regions option, you should always leave the -frames
   option at the default of frame '1'. If you change the frame while
   specifying a region to translate, then the regions will be offset by 1
   or 2 bases, which is not what you want.

Diagnostic Error Messages

   Several warning messages about malformed region specifications:
     * Non-digit found in region ...
     * Unpaired start of a region found in ...
     * Non-digit found in region ...
     * The start of a pair of region positions must be smaller than the
       end in ...

Exit status

   It exits with status 0, unless a region is badly constructed.

Known bugs

   When using the '-regions' option, you should always leave the '-frames'
   option at the default of frame '1'. If you change the frame while
   specifying a region to translate, then the regions will be offset by 1
   or 2 bases, which is not what you want.

See also

   Program name     Description
   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
   coderet          Extract CDS, mRNA and translations from feature tables
   plotorf          Plot potential open reading frames in a nucleotide sequence
   prettyseq        Write a nucleotide sequence and its translation to file
   remap            Display restriction enzyme binding sites in a nucleotide sequence
   showorf          Display a nucleotide sequence and translation in pretty format
   showseq          Display sequences with features in pretty format
   sixpack          Display a DNA sequence with 6-frame translation and ORFs

Author(s)

   Gary Williams formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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

History

   Written 4 March 1999 - Gary Williams
   July 2001 - changed definition of reverse frames to use the same codon
   phase as forward frames. - Gary Williams

   June 2002 - added '-alternative' qualifier - Gary Williams

Target users

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

Comments

   None
