EMBOSS: tranalign

| tranalign

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Generate an alignment of nucleic coding regions from aligned proteins

## Description

tranalign is a re-implementation in EMBOSS of the program mrtrans by Bill Pearson. It reads a set of (unaligned) nucleotide sequences and a corresponding set of aligned protein sequences which are the translations, and writes the coding regions to file as a nucleotide sequence alignment. The sequences must be in the same order in the input sets. Each nucleotide sequence is translated in all three forward frames using the specified genetic code and the translations compared to the corresponding protein sequence from input the alignment. The contiguous nucleotide sequence that coded the protein is written to file (it will not splice together different exons to produce a coding sequence).

## Algorithm

The protein sequences will typically include gap (`-`) characters. These are ignored during sequence comparison but replaced by `---` in the nucleotide sequence alignment output.

## Usage

Here is a sample session with tranalign

    % tranalign ../data/tranalign.pep tranalign2.seq
    Generate an alignment of nucleic coding regions from aligned proteins

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

## Command line arguments

    Generate an alignment of nucleic coding regions from aligned proteins
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-asequence]         seqall     Nucleotide sequence(s) filename and optional
                                      format, or reference (input USA)
      [-bsequence]         seqset     (Aligned) protein sequence set filename and
                                      optional format, or reference (input USA)
      [-outseq]            seqoutset  [.] (Aligned) nucleotide
                                      sequence set filename and optional format
                                      (output USA)

       Additional (Optional) qualifiers:
       -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))

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-asequence" 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
       -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

       "-bsequence" associated qualifiers
       -sbegin2            integer    Start of each sequence to be used
       -send2              integer    End of each sequence to be used
       -sreverse2          boolean    Reverse (if DNA)
       -sask2              boolean    Ask for begin/end/reverse
       -snucleotide2       boolean    Sequence is nucleotide
       -sprotein2          boolean    Sequence is protein
       -slower2            boolean    Make lower case
       -supper2            boolean    Make upper case
       -scircular2         boolean    Sequence is circular
       -sformat2           string     Input sequence format
       -iquery2            string     Input query fields or ID list
       -ioffset2           integer    Input start position offset
       -sdbname2           string     Database name
       -sid2               string     Entryname
       -ufo2               string     UFO features
       -fformat2           string     Features format
       -fopenfile2         string     Features file name

       "-outseq" associated qualifiers
       -osformat3          string     Output seq format
       -osextension3       string     File name extension
       -osname3            string     Base file name
       -osdirectory3       string     Output directory
       -osdbname3          string     Database name to add
       -ossingle3          boolean    Separate file for each entry
       -oufo3              string     UFO features
       -offormat3          string     Features format
       -ofname3            string     Features file name
       -ofdirectory3       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
[-asequence] (Parameter 1) | seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-bsequence] (Parameter 2) | seqset | (Aligned) protein sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
[-outseq] (Parameter 3) | seqoutset | (Aligned) nucleotide sequence set filename and optional format (output USA) | Writeable sequences | <*>.format
Additional (Optional) qualifiers
-table | list | 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
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-asequence" associated seqall qualifiers
-sbegin1 -sbegin_asequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_asequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_asequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_asequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_asequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_asequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_asequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_asequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_asequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_asequence | string | Input sequence format | Any string |
-iquery1 -iquery_asequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_asequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_asequence | string | Database name | Any string |
-sid1 -sid_asequence | string | Entryname | Any string |
-ufo1 -ufo_asequence | string | UFO features | Any string |
-fformat1 -fformat_asequence | string | Features format | Any string |
-fopenfile1 -fopenfile_asequence | string | Features file name | Any string |
"-bsequence" associated seqset qualifiers
-sbegin2 -sbegin_bsequence | integer | Start of each sequence to be used | Any integer value | 0
-send2 -send_bsequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse2 -sreverse_bsequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask2 -sask_bsequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide2 -snucleotide_bsequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein2 -sprotein_bsequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower2 -slower_bsequence | boolean | Make lower case | Boolean value Yes/No | N
-supper2 -supper_bsequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular2 -scircular_bsequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat2 -sformat_bsequence | string | Input sequence format | Any string |
-iquery2 -iquery_bsequence | string | Input query fields or ID list | Any string |
-ioffset2 -ioffset_bsequence | integer | Input start position offset | Any integer value | 0
-sdbname2 -sdbname_bsequence | string | Database name | Any string |
-sid2 -sid_bsequence | string | Entryname | Any string |
-ufo2 -ufo_bsequence | string | UFO features | Any string |
-fformat2 -fformat_bsequence | string | Features format | Any string |
-fopenfile2 -fopenfile_bsequence | string | Features file name | Any string |
"-outseq" associated seqoutset qualifiers
-osformat3 -osformat_outseq | string | Output seq format | Any string |
-osextension3 -osextension_outseq | string | File name extension | Any string |
-osname3 -osname_outseq | string | Base file name | Any string |
-osdirectory3 -osdirectory_outseq | string | Output directory | Any string |
-osdbname3 -osdbname_outseq | string | Database name to add | Any string |
-ossingle3 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo3 -oufo_outseq | string | UFO features | Any string |
-offormat3 -offormat_outseq | string | Features format | Any string |
-ofname3 -ofname_outseq | string | Features file name | Any string |
-ofdirectory3 -ofdirectory_outseq | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-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 | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

The input is a set of unaligned nucleic sequences and the set of aligned protein sequences to be used as a guide in the alignment of the output nucleic sequences.

The ID names of the nucleic acid and protein sequences are NOT checked to see if they correspond to each other. They can have any names.

There must be at least as many protein sequences as nucleic acid sequence - extra protein sequences are ignored.

Each of the nucleic acid sequences must have a corresponding protein sequence which is derived from the coding region of that nucleic acid sequence. The two sets of sequences must be in the same order.

### Input files for usage example

### File: tranalign.seq

    >HSFAU1
    ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
    agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
    cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
    tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc
    tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
    gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
    agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
    cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
    tctaataaaaaagccacttagttcagtcaaaaaaaaaa
    >HSFAU2
    ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
    agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
    cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
    tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc
    tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
    gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
    agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
    cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
    tctaataaaaaagccacttagttcagtcaaaaaaaaaa
    >HSFAU3
    ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
    agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
    cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
    tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
    tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
    gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga
    agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
    cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
    tctaataaaaaagccacttagttcagtcaaaaaaaaaa
    >HSFAU4
    ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
    agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
    cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc
    tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
    tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc
    gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
    agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
    cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
    tctaataaaaaagccacttagttcagtcaaaaaaaaaa
    >HSFAU5
    ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
    agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
    cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
    tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
    tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc
    gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
    agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
    cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
    tctaataaaaaagccacttagttcagtcaaaaaaaaaa

### File: tranalign.pep

    >HSFAU1_3
    PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
    LLAG-PLEDEATLGQCGVEALTTLEVAGRMLG-GKVHGSLARAGKVRGQTPKVAKQEKKK
    KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
    >HSFAU2_3
    PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
    LLAGAPLEDALWASAGWRP
    >HSFAU3_3
    PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
    LLAGAPLEDEATLGQCGVEALTTLEVAGRMLG-GKVHGSLARAGKVRGQTPKGAKQEKKK
    KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
    >HSFAU4_3
    PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHEIASLEGIAPEDQVV
    LLAGAPLEDEATLGQCGVEALTTLEVAGRMLARGKVHGSLARAGKVRGQTPKVAKQEKKK
    KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
    >HSFAU5_3
    PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
    LLAGAPLEDEATLGQCGVEALTTLEVGRMLFG-GKVHGSLARAGKVRGQTPKVAKQEKKK
    KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

## Output file format

### Output files for usage example

### File: tranalign2.seq

    >HSFAU1
    cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
    ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
    cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
    ctcctggcaggc---cccctggaggatgaggccactctgggccagtgcggggtggaggcc
    ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
    gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
    aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
    cccacctttggcaagaagaagggccccaatgccaactct
    >HSFAU2
    cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
    ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
    cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
    ctcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc---
    ------------------------------------------------------------
    ------------------------------------------------------------
    ------------------------------------------------------------
    ---------------------------------------
    >HSFAU3
    cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
    ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
    cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
    ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
    ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
    gcccgtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaag
    aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
    cccacctttggcaagaagaagggccccaatgccaactct
    >HSFAU4
    cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
    ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
    cagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtg
    ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
    ctgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctg
    gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
    aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
    cccacctttggcaagaagaagggccccaatgccaactct
    >HSFAU5
    cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
    ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
    cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
    ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
    ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg
    gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
    aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
    cccacctttggcaagaagaagggccccaatgccaactct

The output is the regions of the nucleic acid sequences which code for the corresponding protein sequence, with gap characters ('-') introduced so that they have the same alignment as the corresponding protein sequences.

## Data files

None.

## Notes

In general, it is better to use protein sequences for multiple alignment, but to use DNA sequences for phylogeny, for example, when using the programs dnadist, dnapars, dnaml, etc in the PHYLIP package. Where one has a protein sequence alignment, it would be time consuming to remove gap characters before back-translating the proteins. tranalign helps by generating aligned cDNA sequences from a protein sequence alignment.

tranalign finds the coding regions for contiguous sequences only. It will not splice together different exons to produce a coding sequence. You should therefore use either mRNA sequences, or nucleic sequences which you have constructed to hold a contiguous coding region (maybe using extractseq or yank and union?).

## References

None.

## Warnings

The sequences must be in the same order in both input sets of sequences. Some alignment program (including clustalw/emma) will re-order their input sequences so as to group similar sequences together.

## Diagnostic Error Messages

"No guide protein sequence available for nucleic sequence xxx" - the corresponding protein sequence for this nucleic sequence has not been input. You have input more nucleic acid sequences than protein sequences.

"Guide protein sequence xxx not found in nucleic sequence xxx" - the region of the nucleic sequence which codes for the protein was not found. The coding region in the nucleic acid sequence must be a single contiguous sequence. The protein sequence might not be the corresponding one for this nucleic acid sequence if they are out of order.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
edialign | Local multiple alignment of sequences
emma | Multiple sequence alignment (ClustalW wrapper)
infoalign | Display basic information about a multiple sequence alignment
plotcon | Plot conservation of a sequence alignment
prettyplot | Draw a sequence alignment with pretty formatting
showalign | Display a multiple sequence alignment in pretty format

## Author(s)

The original program mrtrans was written by Bill Pearson (wrp@virginia.edu)

tranalign was written in EMBOSS code using the description of mrtrans as a guide by 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 © emboss.open-bio.org) not to the original author.

## History

mrtrans written (Jan 1991, July 1987) - Bill Pearson

tranalign written (March 2002) - Gary Williams

## Target users

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

## Comments

None