Usage instructions

Quick start

Paste in or upload DNA sequences and hit "Submit query". The RevTrans server will then virtually translate the DNA sequences and align the resulting peptide sequences using MAFFT with default settings (other alignment program can be selected). Finally RevTrans constructs a multiple DNA alignment using the peptide alignment as a scaffold.

If you want more control over the alignment process RevTrans also accepts user provided peptide alignments. This will give you the opportunity to use your preferred alignment software and to optimize the parameters. If you need to translate your DNA sequences prior to alignment this can be done by using the "Translate only" button (or by following the link to the "Virtual Ribosome" server if you want more fine.grained control over the translation process). The translation has full support for degenerate nucleotides and alternative translation tables can be selected.

When providing your own peptide alignment, RevTrans will accept arbitrarily large input files.

Detailed instructions

Supply DNA sequences

The DNA sequences must either be pasted into the webpage or uploaded via the "Choose file" button. The input must be in FASTA, MSF, or ALN (Clustal) format.

The full IUPAC degenerated DNA alphabet (not case sensitive) is supported:


Please note that gaps and unknown symbolse.g. - and X will be discarded before processing.

Optional: Supply aligned peptide sequences

For greater control of the alignment process you have the option of also supplying a pre-computed peptide alignment. RevTrans will then use this as the scaffold for the DNA alignment. The peptide alignment must be in FASTA, MSF, or ALN (Clustal) format.

By default "-", "." and "~" will be interpreted as gap symbols.

If a peptide alignment is not supplied the RevTrans web-server will automatically construct one using the selected multiple alignment program (deafult: MAFFT). In all case the alignment program will be run with default parameters.

Submit query

Click on the "Submit query" button. If the processing of the query takes more than a few seconds you'll will get the option of supplying your email address and be notified when the job is done.

Advanced options

RevTrans has support for a number of advanced options. Typically it is not necessary to set these manually and most users can safely skip this section and proceed to submitting the query.