SynPlot - Peaks.

Run SynPlot - Peaks

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What is SynPlot?

Synplot - Peaks is a modified version of the Synplot tool available on this web site. It takes as its input (as does Synplot) aligned sequences in FASTA formatted file, with gaps in the sequences introduced by the alignment represented by "-" characters. The sequences must therefore be of the same length.

This implementation takes the scores for each window along the aligned sequence and counts the number of peaks above a user determined similarity score. For details on how the score is derived please goto the Synplot - Background page. As with Synplot part of the alignment may be considered.

Synplot - Peaks returns the number of peaks above a threshold to the screen. A results file (in the GFF format) is also produced that gives details of each peak. This information includes the start and end coordinates (including gaps '-') covered by the peaks and the maximum score for each peak. The numbering can be returned relative to the whole alignment (aligned) or to the first sequence in the alignment, also called the 'reference sequence' (unaligned).

If a GFF formated annotation file is provided for the reference sequence, the output file will show where peaks are present in annotated features, where peaks contain annotated features, or where peaks overlap with annotated features.

The core SynPlot script was designed by Dr. James Gilbert, a former member of this laboratory who is now located at the Sanger Institute. SynPlot is also available as a command line driven script. Modifications were made by Dr. Ian Donaldson.

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