!AAgrphcol v2.0 - FREEWARE - 18/11/02
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 This application loads a drag-and-dropped textfile of single letter amino acid sequence and displays the sequence with the amino acids colour coded according to three categories: Polarity, Charge and Misc.

How to use
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 The application loads an icon onto the iconbar. Simply drop a textfile onto this icon to load it. The program looks for uppercase letters, so make sure the sequence is capitalized. Numbers and lowercase are ignored, so can be left in for extra information.

 With the file loaded, a window will open displaying the sequence. A bar at the  top of the window displays the name of file and the number of amino acids in the sequence as well as 3 radio icons, which can be used to switch between the three categories.

 The rest of the window displays the sequence divided into rows where a one pixel vertical strip represents each amino acid, coloured according to their properties. The absolute number of amino acids and the percent composition of each property is displayed to the right of the sequence in the same colours. Clicking over the sequence with the left mouse button increases the gap between amino acids, which can make things clearer. Clicking the right button will reduce the gap.

The colour coding is as follows:

1) Polarity (Hydrophobicity/hydrophilicity) - Hydrophobic residues are displayed in brown and hydrophilic residues in light blue

2) pH(or charge) - Standard colour coding:  Acid/negative=Red,
Basic/positive=Blue, Neutral=Green

3) Miscellaneous - Cysteine/disulphide=yellow
		   Phosphorylation(Ser, The, Tyr)=blue
		   Aromatic(Phe, Tyr, Trp)=light brown
		   Branched chain(Val, Leu, Ile)=purple

A user-defined property can also be selected. Simply enter the amino acid code(s) you want to highlight in the writable icon and click OK. User-defined residues are displayed in garish pink. The name of the property is initially 'User Type', but this can be changed to whatever you wish (although the length is limited).

The miscellaneous properties can be chosen in any combination by ticking the appropriate icons. Note that if there are clashes between properties (e.g. Tyrosine is both aromatic and phosphorylatible) the later one will be chosen. The user type will always have precedence.
 
Note
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* Further sequences can be loaded by dragging a textfile onto the window, which will resize to fit the sequence

* The maximum size for the sequence is 3000 amino acids. This is fairly arbitrary, but ensures the entire sequence will be visible on a 800x600 display.

MattLB (and DrWimp)
mattlb@angelfire.com  
http://www.angelfire.com/mt/wumps/Bio.html
November 2002
  
  
  
  
  