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Usage instructions



Quick start

Paste in or upload DNA sequences and hit "Submit query". The RevTrans server will then virtually translate the first 75 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.

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 (full support for degenerate nucleotides - alternative translation tables can be selected in the advanced options).

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:

A C G T R Y M K W S B D H V N

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 Dialign2. Dialign2 will be run with default parameters. More information about Dialign2 can be found here.


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.

  • Data format, DNA sequences:
    By default the DNA file format is automatically detected. Alternatively you may specify the format as being FASTA, MSF, or ALN (Clustal).

  • Data format, aligned peptide sequences:
    By default the peptide alignment file format is automatically detected. Alternatively you may specify the format as being FASTA, MSF, or ALN (Clustal).

  • Output format:
    By default the final multiple DNA alignment will be in ALN (Clustal) format. Alternatively you may specify FASTA or MSF.

  • Gap-In:
    Here you can specify which symbol(s) denote(s) a gap in user provided peptide alignemnt. The default should be correct for virtually all standard alignment files.

  • Gap-out:
    Here you can specify which gap symbol to use in the output.

  • Match DNA and peptide sequences by:
    This option gives the user control over how DNA sequences paired to their peptide counterpart.

    • Translation:
      (Default) The DNA sequences are translated using the standard genetic code (or an alternative translation table if selected below) with full IUPAC support and compared to the peptide sequences. The DNA sequence is paired with the first matching peptide sequence found.

    • Name:
      DNA sequences are paired with peptide counterparts based on sequence entry names. Entry names must be unique within files and identical across files. If you experience trouble when using name based matching, please make sure that sequences names do match across files as some alignment software may truncate or otherwise alter sequence names.

    • Position:
      DNA sequences are paired with peptide counterparts simply based on their order of appearance in the files.

  • Translation table:
    Select an alternative translation table - used for "matching-by-translation" and with the "Translate Only" functionality.

    The numbering of the translation table is the one defined by the NCBI Taxonomy Group. For a detailed description of each genetic code, please consult the following web page at NCBI: The Genetic Codes . [Main site: Taxonomy]

  • Alignment method
    (New in RevTrans 1.4) RevTrans offers a selected of programs for performing the peptide alignment step:

    • Dialign 2.2:

      Reference:
      B. Morgenstern (1999).
      DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
      Bioinformatics 15, 211 - 218.

    • Dialign-T 0.1.3:

      Reference:
      Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern:
      DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
      Bioinformatics 2005, 6:66.

    • ClustalW 1.83:

      Reference:
      Higgins D., Thompson J., Gibson T. Thompson J. D., Higgins D. G., Gibson T. J.(1994).
      CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice.
      Nucleic Acids Res. 22:4673-4680.




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