EMBOSS: transeq

| ## EMBOSS: transeq

# Program transeq

## Function

Translate nucleic acid sequences

## Description

This translate 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 corersponding 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

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

    % transeq pop.seq pop.pep

To translate a sequence 'pop.seq' in the second frame:

    % transeq pop.seq pop.pep -frame=2

To translate a sequence 'pop.seq' in the third frame in the reverse sense (starting at the last base and proceeding to the start):

    % transeq pop.seq pop.pep -frame=-1

To translate a sequence 'pop.seq' in all three forward frames:

    % transeq pop.seq pop.pep -frame=F

To translate a sequence 'pop.seq' in all three reverse frames:

    % transeq pop.seq pop.pep -frame=R

To translate a sequence 'pop.seq' in all six forward and reverse frames:

    % transeq pop.seq pop.pep -frame=6

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

    % transeq pop.seq pop.pep -reg=2-45,67-201,328-509

To translate a sequence 'mito.seq' using the mammalian mitochondrion genetic code table:

    % transeq mito.seq mito.pep -table=2

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers:
       -frame              menu       Frame(s) to translate
       -table              menu       Code to use
       -regions            range      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               bool       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 *

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
-frame | Frame(s) to translate |
1 | (1)
2 | (2)
3 | (3)
F | (Forward three frames)
-1 | (-1)
-2 | (-2)
-3 | (-3)
R | (Reverse three frames)
6 | (All six frames)
| 1
-table | Code to use |
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)
| 0
-regions | 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 | Sequence range | Whole sequence
-trim | 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 * | Yes/No | No
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The input sequence can be one or more nucleic acid sequences.

## Output file format

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'.

For example, the result of the command
transeq em:hsfau -frame=6
would be:

    >HSFAU_1 H.sapiens fau mRNA
    FLFLDSIFAVAGTAVQSPICSSLSAPRSYTPSR*PARKRSPRSRLM*PHWRALPRKIKSC
    SWQARPWRMRPLWASAGWRP*LPWK*QAACLEVKFMVPWPVLEK*EVRLLRWPNRRRRRR
    RQVGLSGGCSTTGALSTLCPPLARRRAPMPTLKSFVILAFSNKKAT*FSQKKX
    >HSFAU_2 H.sapiens fau mRNA
    SSFSTPSSR*LGPPFSRQYAALCPRPGATHLRGDRPGNGRPDQGSCSLTGGHCPGRSSRA
    PGRRAPGG*GHSGPVRGGGPDYPGSSRPHAWR*SSWFPGPCWKSERSDS*GGQTGEEEEE
    DRSG*AADAVQPALCQRCAHLWQEEGPQCQLLSLL*FWLSLIKKPLSSVKKKX
    >HSFAU_3 H.sapiens fau mRNA
    PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVL
    LAGAPLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKK
    TGRAKRRMQYNRRFVNVVPTFGKKKGPNANS*VFCNSGFL**KSHLVQSKKK
    >HSFAU_4 H.sapiens fau mRNA
    FFLTELSGFFIRESQNYKRLKSWHWGPSSCQRWAQR*QSAGCTASAA*PDLSSSSSSPVW
    PP*ESDLSLFQHGPGNHELYLQACGLLLPG*SGPPPRTGPEWPHPPGARLPGARLDLPGQ
    CPPVRLHEP*SGRPFPGRSPRRCVAPGRGQRAAYWRLNGGPSYREDGVEKEE
    >HSFAU_5 H.sapiens fau mRNA
    FFFD*TKWLFY*RKPELQKT*ELALGPFFLPKVGTTLTKRRLYCIRRLARPVFFFFFSCL
    ATLGV*PLTFPARAREP*TLPPSMRPATSRVVRASTPHWPRVASSSRGAPARSTT*SSGA
    MPSSEAT*ALIWATVSWPVTSKVCSSWARTKSCILATERRSQLPRRWSRERGX
    >HSFAU_6 H.sapiens fau mRNA
    FFF*LN*VAFLLEKARITKDLRVGIGALLLAKGGHNVDKAPVVLHPPLSPTCLLLLLLLF
    GHLRSLTSHFSSTGQGTMNFTSKHAACYFQGSQGLHPALAQSGLILQGRACQEHDLIFRG
    NALQ*GYMSLDLGDRFLAGHLEGV*LLGADKELHIGD*TAVPATAKMESRKRX

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 EMBOSS environment variable EMBOSS_DATA.

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

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 reverse frame '-1' is defined as the translation you get when you use the reverse-complement of the sequence withthe same codon phase as the codon in frame '1'.

Thus the sequence ACTGG in 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'.

Before version 2.0.0 transeq used the alternate way of generating the reverse translation frames which is that frame -1 is made by taking the frame '1' of the reverse complement.

There does not appear to be a convention on which definition to use.

The current definition makes it slightly simpler to generate peptides to align under sequences when displaying translation in all 6 frames. It appears to be the definition used by the majority of other sequence analysis packages. The switch to the current definition was therefore made.

## References

None.

## Warnings

When translation using non-standard genetic code table, always 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
--- | ---
backtranseq | Back translate a protein sequence
coderet | Extract CDS, mRNA and translations from feature tables
plotorf | Plot potential open reading frames
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
showorf | Pretty output of DNA translations
showseq | Display a sequence with features, translation etc

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## 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

## Target users

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

## Comments