SynPlot.

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Example Files

References

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SynPlot Instructions.

Input files.
Configuration file.
The name of a file which specifies the colour and width of rectangles representing the <features>, which are drawn on top of the sequences, and the order in which they are drawn. This file is in Perl language format, and an example ("default.conf") is included in the 'Example Files' page of the web-site.

For further instructions on writing your own configuration file, please follow the [LINK]

Sequence alignment file.
As described the 'Background' page of this web-site, the aligned sequences must be present in a single FASTA format file. All the sequences must be of the same length. Gaps are represented by '-'. The header, denoted by '>' must be present on its own line (no spaces), e.g.

      >header1
      ACTG-GAA...etc
      
      >header2
      ACTG-GAA...etc

      >header3
      ACTG---A...etc
      
Please note that the last nucleotides of sequences should be on the last line of the file.

GFF feature format files.
For each sequence header extracted from the FASTA global alignment file, SynPlot will look for a file NAME.gff, (where NAME is the name found in the header).

The GFF format is explained at the Sanger Institute. We recommend two methods for creating GFF files for your own sequences [LINK].

Output picture options:
Window size.
Specify the size of the window which is moved along the identity string.

Window sliding increment.
Specify how far the window is moved between samples.

Picture orientation.
Specify whether the final figure is in the landscape or portrait orientation.

Border size.
The number of points of space between the edge of the paper and the figure.

Nucleotides per line.
Sets the width of each line of the aligned sequence on the figure (in nucleotides).

Beginning and end of alignment.
Set the range of nucleotides in the alignment to be displayed.

Picture format.
Specify whether the final figure is in postscript or PDF format.

SynPlot Troubleshooter.

Features are being displayed, but they are all black....
This is likely to be a problem with the format of the configuration file. Check that the features described in the configuration file are spelt exactly the same in the GFF files. The feature name in the GFF file and configuration file must be in the same case, i.e. Cds and CDS will not match! Follow [LINK] for more information.

A plot is produced, but there are no features....
This is likely to be a problem with one or more of the GFF files. There are several common mistakes to be aware of:
  • The GFF files should be named exactly as the sequence headers in the global alignment. For example, in the alignment file >human should have a corresponding GFF file named human.gff.
  • In the GFF file the first column <seqname> should be exactly the same as GFF file name and the header of the global alignment file.
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