Peak Extractor.

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Peak Extractor Instructions.

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

      >header1
      sequence 1...
      
      >header2
      sequence 2...

      >header3
      sequence 3...
      
Please note that the last nucleotides of sequences should be on the last line of the file.

Options:
Choose the range of the global aligment you want to be extracted.
Specify the start and the end of the range of nucleotides you wish to extract from the global alignment. For example, this information can be obtained from a SynPlot plot. A web tool is available from this web site.

Select whether you want to see the extracted sequence in a plain text format or formatted using PRETTYPLOT.
The extracted output can be retreived as a plain text file (in FASTA format). This format can be used in other display utilities. However, the alignment can also be formatted using the EMBOSS program PRETTYPLOT.

PRETTYPLOT options:
Select to view the consensus sequence for you alignment.
A consensus sequence may also be displayed with the extracted region. Consensus nucleotides are selected if one nucleotide is present greater than (number of sequences / 2) + 0.5 - rounded up to the next integer. These nucletides corresspond to the blocks with a black background.

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

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