| tranalign

## Function

Align nucleic coding regions given the aligned proteins

## Description

tranalign is a re-implementation in EMBOSS of the program mrtrans by Bill Pearson.

tranalign is a simple program that allows you to produce aligned cDNA sequences from aligned protein sequences. This can be very useful for phylogeny programs, e.g. in PHYLIP - dnadist, dnapars, dnaml, etc. In general, it is better to use protein sequences for multiple alignments, but to use DNA sequences for phylogeny. This can be time consuming when there are gaps in the aligned protein sequences.

tranalign takes a set of (unaligned) nucleic sequences and a set of aligned protein sequences. It reads the first nucleic sequence and the first protein sequence, translates the nucleic sequence in each of the three forward frames, compares the protein sequence to the translated nucleic sequence to find the protein coding region, and then writes out the nucleic sequence that encoded the protein.

The sequences must be in the same order in both sets of sequences. A common problem you should be aware of is that some alignment program (including clustalw/emma) will re-order the aligned sequences to group similar sequences together.

The protein library may include '-' characters to specify alignments. Each '-' character in the protein library is ignored during the sequence comparison but replaced by '---' in the nucleic sequence output to form the aligned nucleic sequences.

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?).

## Usage

Here is a sample session with tranalign

    % tranalign ../data/tranalign.pep tranalign2.seq
    Align nucleic coding regions given the aligned proteins

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

## Command line arguments

       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
       -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

       "-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
       -sformat2           string     Input sequence format
       -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 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-asequence] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-bsequence] (Parameter 2) | (Aligned) protein sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
[-outseq] (Parameter 3) | (Aligned) nucleotide sequence set filename and optional format (output USA) | Writeable sequences | <*>.format
Additional (Optional) qualifiers | Allowed values | Default
-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
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## 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

The sequences must be in the same order in both sets of sequences. A common problem you should be aware of is that some alignment program (including clustalw/emma) will re-order the aligned sequences to group similar sequences together.

## References

None.

## Warnings

None.

## 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 alignment program - interface to ClustalW program
infoalign | Information on a multiple sequence alignment
plotcon | Plot quality of conservation of a sequence alignment
prettyplot | Displays aligned sequences, with colouring and boxing
showalign | Displays a multiple sequence alignment

## 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 (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## 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