Difference between revisions of "Pepwheel"

Revision as of 07:41, 7 September 2007

pepwheel is a bioinformatics tool to visualise protein sequences as helices. It is part of the EMBOSS package.

Usage

Input

The input is a protein sequence in FASTA format.

Output Options

Number of steps 

The number of residues plotted per turn is this value divided by the 'turns' value.

Number of turns 

The number of residues plotted per turn is the 'steps' value divided by this value.

Amphipathic residue marking 

If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'.

Mark as squares 

By default the aliphatic residues ILVM are marked with squares.

Mark as diamonds 

By default the residues DENQST are marked with diamonds.

Mark as octagons 

By default the positively charged residues HKR are marked with octagons.

Graphical output

Format to use for graphics output:

• Portable Network Graphic (png)
• Colour PostScript (cps)
• Black and White Postscript (ps)
• Hewlett-Packard Graphics Language (hpgl)
• Plot data (data)

Example

The following is for the protein sequence of 1fin.

• Input commands:

pepwheel -sequence '1fin.fa' $tmpSFormatOpt -wheel Y -steps 18 -turns 5 \
  -amphipathic N -squares 'ilvm' -diamonds 'denqst' -octags 'hkr' \
  -graph 'png' -goutfile '1fin.pepwheel.png' -auto

• Graphical output:

File:1fin.pepwheel.png