Pepwheel - Revision history

Christoph at 00:58, 10 July 2012

2012-07-10T00:58:47Z

Christoph: /* Example */

2007-09-07T07:41:18Z

‎Example

Christoph at 07:39, 7 September 2007

2007-09-07T07:39:01Z

New page

'''pepwheel''' is a [[:Category:Bioinformatics|bioinformatics]] tool to visualise protein sequences as helices. It is part of the [[:Category:EMBOSS|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 <code>ACFGILMVWY</code> are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '<code>-squares</code>', '<code>-diamonds</code>' and '<code>-octags</code>'.
;Mark as squares :By default the aliphatic residues <code>ILVM</code> are marked with squares.
;Mark as diamonds :By default the residues <code>DENQST</code> are marked with diamonds.
;Mark as octagons :By default the positively charged residues <code>HKR</code> are marked with octagons.

===Graphical output===
Format to use for graphics output:

*[[PNG|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 [http://www.rcsb.org/pdb/explore/explore.do?structureId=1FIN 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

[[Category:EMBOSS]]

@@ Line 31: / Line 31: @@
 *Graphical output:
-[[Image:1fin.pepwheel.png]]
+<!--[[Image:1fin.pepwheel.png]]-->
 [[Category:EMBOSS]]

@@ Line 29: / Line 29: @@
     -amphipathic N -squares 'ilvm' -diamonds 'denqst' -octags 'hkr' \
     -graph 'png' -goutfile '1fin.pepwheel.png' -auto
 [[Category:EMBOSS]]