Prettyprinting DNA sequences

Prettyprinting DNA sequences

[Johannes Huesing]

Hi all, 

as it has become hip to fill publications with long strings of capital
letters from the set {A, C, G, T}, I would like to know how difficult
it is to have them prettyprinted, i.e. make A, C, G, T active
characters that are printed out in red (A), blue (G), yellow (C) and
green (T), respectively, and that are broken like regular words i.e. a
line can be broken after each letter.

Do you think this would be feasible?

Greetings

Johannes
-- 
Johannes Hüsing | Domain: Adresse im Internet. Besteht aus einem 
hannes@ruhrau.de| technischen Teil (http://www.), einem Namen 
                | (erwin_meier) und einer Endung  (zum Beispiel 
                | .de für Deutschland) [J. Albrecht, "Zeit" 12/2001]

Re: Prettyprinting DNA sequences

[Hans Hagen]

At 07:23 PM 5/24/01 +0200, Johannes Huesing wrote:
>Hi all, 
>
>as it has become hip to fill publications with long strings of capital
>letters from the set {A, C, G, T}, I would like to know how difficult
>it is to have them prettyprinted, i.e. make A, C, G, T active
>characters that are printed out in red (A), blue (G), yellow (C) and
>green (T), respectively, and that are broken like regular words i.e. a
>line can be broken after each letter.
>
>Do you think this would be feasible?

well, fortunately this is quite simple to do, 

\def\dnasymbol#1#2%
  {\unskip 
   {\localcolortrue\tttf#1#2}% local colors are much faster with many
colors per page  
   \hskip0pt plus 1pt minus 1pt % that way we can break and get no
over/underfull lines
   \ignorespaces}

\def\dnasequence #1#2#3#4 % space or line delimited 
  {\dnasymbol\red   #1%
   \dnasymbol\green #2%
   \dnasymbol\blue  #3%
   \dnasymbol\yellow#4}

\def\startdnasequence% watch out,\stopDNAsequence would fail now 
  {\bgroup
   \defineactivecharacter A {\dnasymbol\red    A}%
   \defineactivecharacter C {\dnasymbol\green  C}%
   \defineactivecharacter G {\dnasymbol\blue   G}%
   \defineactivecharacter T {\dnasymbol\yellow T}}

\def\stopdnasequence% so we use lowercase names 
  {\egroup}

\setupcolors[state=start]

\starttext

\dnasequence ACGT
\dnasequence ACGT
\dnasequence ACGT
\dnasequence ACGT
\dnasequence ACGT
\dnasequence ACGT
\dnasequence ACGT

\startdnasequence
ACGT ACGT ACGT ACGT ACGT ACGT ACGT
\stopdnasequence

\stoptext

As you can see, my genome is quite simple, but don't patent it, 

I'm sure that others can come up with alternatives; it also depends on the
way you provide the input. 

Hans

PS. Of course you can make a random generator [possible in context]. 
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