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RevTrans 1.4 Server

[NOTICE: New improved version is now open for testing: RevTrans 2.0]

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 1.4: Improvements in the transcription model, restriction on 75 sequences removed, more alignments programs: Dialign 2, Dialign-T and ClustalW, - [Previous version: RevTrans 1.3]

Instructions Output format Background Software download Article abstract

Paste in DNA sequences

Upload file containing DNA sequences


Optional: Paste in peptide alignment

Optional: Upload peptide alignment


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

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 Dialign2 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.

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

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


Advanced options

Data format, DNA sequences

Automatic
FASTA
MSF
ALN (Clustal format)
Any gaps will be removed

Data format, aligned peptide sequences

Automatic
FASTA
MSF
ALN (Clustal format)

Output format

FASTA
MSF
ALN (Clustal format)

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: "-".

Translation table:


First codon is start codon
All codons are internal

The translation tables are adapted from the NCBI taxonomy web site.

For a detailed description of each genetic code, please consult the following web page at NCBI: The Genetic Codes . [Main site: Taxonomy]

Alignment method


Troubleshooting

Verbose

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.

Restrictions: If no peptide alignment is present the RevTrans server will produce one by translating the DNA sequences and running dialign2 with standard settings. RevTrans will accept abitrary large input if you supply your own alignment.

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 1.3 is free software and can be downloaded from here. The command line version RevTrans is without the integration with Dialign2.

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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