| ## EMBOSS: tranalign

# Program 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 tranalign.seq tranalign.pep tranalign2.seq

## Command line arguments

       Mandatory qualifiers:
      [-nsequence]         seqall     Nucleotide sequences to be aligned
      [-psequence]         seqset     Protein sequence alignment
      [-outseq]            seqoutset  Output sequence set USA

       Optional qualifiers:
       -table              menu       Code to use

       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
--- | --- | ---
[-nsequence] (Parameter 1) | Nucleotide sequences to be aligned | Readable sequence(s) | Required
[-psequence] (Parameter 2) | Protein sequence alignment | Readable sequences | Required
[-outseq] (Parameter 3) | Output sequence set USA | Writeable sequences | <sequence>.format
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 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.

## Output file format

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
--- | ---
emma | Multiple alignment program - interface to ClustalW program
infoalign | Information on a multiple sequence alignment
plotcon | Plots the 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 by Gary Williams using the description of mrtrans as a guide (gwilliam@hgmp.mrc.ac.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