transeq.txt

emboss的linux版本的源代码

                                  transeq 



Function

   Translate nucleic acid sequences

Description

   Transeq translates nucleic acid sequences to the corresponding peptide
   sequence.

   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.

   It can translate specified regions 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.

   Termination (STOP) codons are translated as the character '*'.

   The output peptide sequence is always in the standard one-letter IUPAC
   code.

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:paamir 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:paamir 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:paamir 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:paamir 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:paamir 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:paamir 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:paamir 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

   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.

   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
   -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

   "-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 standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   transeq reads one or more nucleic acid sequence USAs.

  Input files for usage example

   'tembl:paamir' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:paamir

ID   PAAMIR     standard; DNA; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
SV   X13776.1
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas
.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
RN   [2]
RP   1167-2167
RX   MEDLINE; 89211409.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomona
s
RT   aeruginosa";
RL   FEBS Lett. 246:39-43(1989).
XX
RN   [3]
RP   1-1292
RX   MEDLINE; 91317707.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product.";
RL   J. Bacteriol. 173:4914-4921(1991).