desc of "blue is for basic" - seq app color file

Jeremy John Ahouse ahouse at hydra.rose.brandeis.edu
Wed Jun 23 12:42:22 EST 1993

    When Don Gilbert asked for suggestions for good colors for amino acids
in the new seqApp Phil Carl made a suggestion and I made a color file for
them.  Don included it in the current version as "Blue is for Basic."  Any
of you who are using the new seqApp may wonder what the other colors are
"for", so here is a recap.

                            ---- cut here ----

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))

Blue for basic amino acids; Lys, Arg, His
(blue and basic both start with "b")

White for hydroxyl amino acids; Ser, Thr (as in whitewater) 
(this was not possible so I chose a cool "whitewater" color - JJA)

Green for amide amino acids; Asn and Gln 
(since glutamine and asparagine rhyme with green)

Yellow for sulphur amino acids; Cys, Met
(this one's obvious)

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)

Orange for aromatic amino acids; Tyr, Phe, Trp 
(since "orange" sounds a little like "aromatic" and 
oranges are aromatic (if that suits you better))

Purple for proline; Pro
(since both have "prl" in them)

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

        Jeremy John Ahouse
        Center for Complex Systems and Biology Dept
        Brandeis University
        Waltham, MA 02254-9110
        (617) 736-4954
        email: ahouse at hydra.rose.brandeis.edu
        Mail from Mac by Eudora 1.3.1 - RIPEM accepted

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