SynPlot - Peaks.

Run SynPlot - Peaks

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SynPlot - Peaks Instructions.

Input files.
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 file for the reference sequence.
The GFF format is explained at the Sanger Institute. We recommend two methods for creating GFF files for your own sequences [LINK]. The numbering should be relative to the first sequence in the alignment (not including gaps).

Minimum identity.
Specify a score that peak scores must be equal to, or exceed. The default score is 0.75 (75% pair-wise sequence identity).

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.

Beginning and end of alignment.
Set the range of nucleotides in the whole alignment from which to locate peaks.

Receive number relative to the whole alignment (aligned) or the reference sequence (unaligned).
Coordinates for the peaks can be set as aligned or unaligned.

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