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RevTrans 2.0 Server - beta

[Previous version: RevTrans 1.4 - feedback and bug reports about version 2.0 are much welcome: raz@cbs.dtu.dk and gorm@cbs.dtu.dk]

RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.

New in RevTrans 2.0: Integration with Virtual Ribosome for translation and ORF finding, visualization of alignments using JalView, more alignments programs: MAFFT, T-COFFEE, Dialign 2, Dialign-T and ClustalW2. Improved tab-based interface.

Instructions Output format Background Software download Article abstract

Paste in DNA sequences

Upload file containing DNA sequences


View example DNA sequences

Optional: Paste in peptide alignment

Optional: Upload peptide alignment


View example peptide alignment
Valid formats: FASTA, MSF and ALN (Clustal) - any gaps will be removed from DNA sequences

Alignment method

Translation table:


Translate from position 1
ORF finder: require ATG start codon.
ORF finder: require any start codon (ATG, TTG, CTG in the standard code).
ORF finder: do not require a start codon.

The translation is performed using the VirtualRibosome software. For more fine-grained control of the translation process (including advanced settings for the ORF finder), please follow this link to the VirtualRibosome server.

Gap-In

Characters defined as gaps in the input files.


Leave blank to use default settings: ".-~".

 

Match DNA and peptide sequences by:

Translation
Name
Position

Gap-Out

Character to use as gap indicator in the final DNA alignment.


Leave blank to use default settings: "-".

RevTrans can generate several levels of verbose rapports

This is especially useful for debugging issues were the corresponding DNA/Peptide sequences are not matched correctly.

Level 0: Error messages only (Default)
Level 1: Info about files/input, number of sequences read etc.
Level 2: As level 1 + Print detailed info about all the sequence names
Level 3: As level 2 + Do a sanity check on the degapped lenght of the sequences. Warn if the sizes do not match.

Instructions: Paste in or upload DNA sequences and hit "Submit query". The RevTrans server will then virtually translate the sequences and align the resulting peptide sequences using MAFFT with default settings. Finally RevTrans constructs a multiple DNA alignment using the peptide alignment as a scaffold. The translation process is by default done using the Standard Genetic Code (alternative translation tables can be selected) and has support for the full IUPAC alphabet of degenerate nucleotides.

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 above.

Please read the CBS access policies for information about limitations on the daily number of submissions.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.


CITATIONS

For publication of results, please cite:

Rasmus Wernersson and Anders Gorm Pedersen.
RevTrans - Constructing alignments of coding DNA from aligned amino acid sequences.
Nucl. Acids Res., 2003, 31(13), 3537-3539.

View the abstract.


PORTABLE VERSION

Would you prefer to run RevTrans at your own site? The command line version of RevTrans is free software and can be downloaded from here. The command line version RevTrans is without the integration with the alignment programs.

The RevTrans web-server is available as a package on a commercial license. Currently available platforms include MIPS (under IRIX, Silicon Graphics), Pentium family (Linux) and most other UNIX based systems. Send inquiries by e-mail to software@cbs.dtu.dk.


GETTING HELP

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