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Color Selections

You can create your own color selection for alignment display by choosing the Nucleic codes or Amino codes dialogs from the Sequence menu. These dialogs provide color "buttons" for each base. Click a button to get a color picker dialog where you can change the currently assigned color. Your selection can be saved to disk file as an amino color or a nucleic color document. You can reload such a color scheme by clicking open this document, or by choosing it from the File "Open..." dialog.

A few early users of this new version provided two of the color amino selections that ship with SeqPup. Here are their descriptions.

Date: Fri, 28 May 1993 20:07:26 -0500

From: ahouse@hydra.rose.brandeis.edu (Jeremy John Ahouse)

Subject: implemented aa colors for pre-rel seqApp

Don Gilbert (& Phil Carl),

I have implemented Phil Carl's(*) modest proposal.

Some of the suggestions were not possible, so I made changes.

Jeremy Ahouse

Phil's suggestion is interspersed with my additions:

Well, I have (as they say) a modest suggestion. I suppose what people

are really seeking are 20 colors for 20 amino acids. I have a preliminary

proposal based on classifying the amino acids into chemical groups and

finding what seems to me to be easy pneumonics for each group. Thus

I would propose:

Red for acidic amino acids; Glu, Asp

(since red is a common danger signal and acids are dangerous

(well maybe not amino acids, but it's a start))

hue: 65500

saturation: 65000

brightness: 50000

Blue for basic amino acids; Lys, Arg, His

(blue and basic both start with "b")

hue: 44000

saturation: 65000

brightness: 50000

White for hydroxyl amino acids; Ser, Thr (as in whitewater)

(this was not possible so I chose a cool "whitewater" color)

hue: 33000

saturation: 65000

brightness: 50000

Green for amide amino acids; Asn and Gln

(since glutamine and asparagine rhyme with green)

hue: 22000

saturation: 65000

brightness: 50000

Yellow for sulphur amino acids; Cys, Met

(this one's obvious)

hue: 12000

saturation: 65000

brightness: 60000

Black for hydrophobic amino acids; Ala, Val, Leu, Ile

(Black is the opposite of white and so if white is for hydrophilic

hydroxyl amino acids black is a natural for hydrophobic ones)

hue: 00000

saturation: 00000

brightness: 00000

Orange for aromatic amino acids; Tyr, Phe, Trp

(since "orange" sounds a little like "aromatic" and

oranges are aromatic (if that suits you better))

hue: 7000

saturation: 65000

brightness: 60000

Purple for proline; Pro

(since both have "prl" in them)

hue: 51000

saturation: 65000

brightness: 60000

Grey for glycine; Gly

(since both start with "g" and grey is sort of blah-like glycine)

hue: 00000

saturation: 00000

brightness: 30000

*Phil Carl

Assoc. Director

Program in Molecular Biology and Biotechnology

University of North Carolina, Chapel Hill

======================

Date: Mon, 7 Jun 1993 15:50:09 +0200

From: Heikki.Lehvaslaiho@Helsinki.FI (Heikki Lehvaslaiho)

Subject: aa colors

Hi,

I am including a file with amino acid color codes that are used in Steven

Smith's GDE. This scheme was not mentioned in the Usernet discussion, but

I've grown accustomed to it. At least, it is no worse that any other of the

myriad possible coloring choices.

If you haven't got other schemes in files yet, drop me a note and I'll see

what I can do.

GDE aa-colors:

2 4 - b i t M a c

COLOR AA R G B R G B

---------------------------------------------------------------------

Magenta AGPST 255 000 255 65535 0 65535

Black BDENQZ 000 000 000

Red C 225 000 000 57600 0 0

Blue FWY 000 000 255 0 65535 65535

Light blue HKR 000 192 192 0 49344 49344

Green ILMV 000 192 000 0 49344 0

Gray JOUX 145 145 145 37265 37265 37265

-Heikki


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