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Display Nucleotides As Color

Hi,

Is there an easy way to display a sequence like "ATCC" as "red blue green green" colors on a figure, when red = A, blue = T, and green = C? I am thinking something like a heatmap in R if I can assign color to discrete values. Thanks.

nucleotide
• 9,912 views • link
updated by Ibrahim Tanyalcin Ibrahim Tanyalcin • written by John John

7 answers

Ugly & quick HTML hack:

  • paste your sequence on a file, e.g. seq.dna

  • transform it to HTML, e.g. through sed:

    sed 's/[ACTG]/&<\/span>/gi' seq.color > seq.html

  • Attach a stylesheet to it, e.g.:

    <head>
<style TYPE="text/css"> 
  .A {
     color: red;
     background: red;
     font-family: monospace;
     font-size: 40px;
  }
  .C {
     color: green;
     background: green;
     font-family: monospace;
     font-size: 40px;
  }
  .G {
     color: orange;
     background: orange;
     font-family: monospace;
     font-size: 40px;
  }
  .T { 
     color: blue;
     background: blue;
     font-family: monospace;
     font-size: 40px;
  }
</style>
</head>

  • The result file should look like:

    <head>
<style TYPE="text/css"> 
  .A {
     color: red;
     background: red;
     font-family: monospace;
     font-size: 40px;
  }
  .C {
     color: green;
     background: green;
     font-family: monospace;
     font-size: 40px;
  }
  .G {
     color: orange;
     background: orange;
     font-family: monospace;
     font-size: 40px;
  }
  .T { 
     color: blue;
     background: blue;
     font-family: monospace;
     font-size: 40px;
  }
</style>
</head>

<span class="A">A</span><span class="G">G</span><span class="G">G</span><span class="C">C</span><span class="T">T</span><span class="T">T</span><span class="T">T</span><span class="A">A</span><span class="G">G</span><span class="t">t</span><span class="g">g</span><span class="c">c</span><span class="A">a</span>

  • Open in a web browser

  • example
• 1 views • link
updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

@John: ah, ok! well, you can simply add a background of the same color. I'll update the examples.

• 0 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Thanks Giovanni!

• 0 views • link
written by John John

Sorry, I forgot that you should also use a Monospace font.

• 0 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Well... I'm not sure what you mean by "on a figure", but in the past, I've done this with HTML like Giovanni said or (slightly dumber) with a script that puts a <font color=\"#FF0000\"></font> around all A's or whatever.

In R, you can use the text() command to put text on a plot or just use pch='A' and color='red' to make points on a plot red A's, for example.

seq<-"ATCGTACG"
seqlist<-strsplit(seq,"")
cols<-c('red','blue','green','purple')
plot(1:length(seqlist[[1]]),rep(1,times=length(seqlist[[1]])),pch=seqlist[[1]],col=cols[factor(seqlist[[1]])])

This would take some fiddling for a longer sequence, but you get the idea.

EDIT: after reading your comment above, it's actually easier.

seq<-"ATCGTACG"
seqlist<-strsplit(seq,"")
cols<-c('red','blue','green','purple')
image(matrix(as.numeric(factor(seqlist[[1]]))),col=cols)
• 0 views • link
updated by Ram Ram • written by Madelaine Gogol Madelaine Gogol

Thanks. I will try it.

• 0 views • link
written by John John

A quick hack (not fully tested, but you'll get the idea): the following C program will generate a postscript file with the colored rectangles:

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <ctype.h>

int main(int argc,char** argv)
    {
    int i,j,k,n;
    double SIZE=500.0;
    double side=0;
    int c;
    int len=0;
    char* s=malloc(sizeof(char));

    if(s==NULL) return EXIT_FAILURE;
    while((c=fgetc(stdin))!=EOF)
        {
        if(isspace(c)) continue;
        s=realloc(s,sizeof(char)*(len+2));
        if(s==NULL)
            {
            fprintf(stderr,"Out of memory\n");
            return EXIT_FAILURE;
            }
        s[len++]=c;
        }
    s[len]=0;
    if(len==0) return EXIT_FAILURE;
    n=ceil(sqrt(len));
    side=SIZE/n;
    k=0;
    printf("%%!PS\n");
    printf("/dside 100 def\n");
    printf("/box { 2 dict begin /y exch def /x exch def "
        "newpath " 
        "y dside mul x dside mul moveto "
        "dside 0 rlineto "
        "0 dside rlineto "
        "dside -1 mul 0 rlineto "
        "0 dside -1 mul rlineto "
        "closepath "
        "fill "
        "  end} bind def\n");
    printf("/red   {  1 0 0 setrgbcolor  box } bind def\n");
    printf("/green {  0 1 0 setrgbcolor  box } bind def\n");
    printf("/blue  {  0 0 1 setrgbcolor  box } bind def\n");
    printf("/yellow  {  1 0 1 setrgbcolor  box } bind def\n");
    printf("/black {  0 0 0 setrgbcolor  box } bind def\n");
    for(i=0;i< n && k<len;i++)
        {
        for(j=0;j<n && k<len;++j)
            {
            printf("%d %d",i,j);
            switch(toupper(s[k++]))
                {
                case 'A': fputs(" red\n",stdout); break;
                case 'T': fputs(" green\n",stdout); break;
                case 'C': fputs(" yellow\n",stdout); break;
                case 'G': fputs(" blue\n",stdout); break;
                default: fputs(" black\n",stdout); break;
                }
            }
        }
    printf("showpage\n");
    return 0;
    }

Compilation:

gcc -o biostar12763 -Wall source.c -lm

Execution:

echo "ATAGCTAGCATCAGTCTAGCTTAGCTAGCGCNNACTAGCT" | ./biostar12763   > file.ps
ghostview file.ps ## or evince file.ps or... etc...
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

JalView is excellent for creating figures of proteins and nucleotides. Even if you do not have an alignment, you can still enter a single sequence. Lots of export options as well including wrapped text and export to a pdf.

• 1 views • link
written by Alastair Kerr Alastair Kerr

Thanks. A little different than what I want.

• 0 views • link
written by John John

I don't know how to make this with R, but I think you can open the sequences with mega or clustalX, in which the nucleotides are colored, and then get a screenshot.

• 0 views • link
written by Yumtaoist • Yumtaoist

Thanks for the suggestion. I am trying to make this into a pipeline. Fewer separate programs would be better for me.

• 0 views • link
written by John John

This is pretty hacktastic, but I don't know a better way

library(ggplot2)
dna <- "ATAGCATCGACTAG"
bases <- unlist(strsplit(dna, ""))
col_scheme <- c("red", "green", "yellow", "blue")
names(col_scheme) <- c("A", "T" ,"C", "G")
p <- qplot(1:length(bases), 1, fill=col_scheme[bases])
p + geom_tile() + scale_fill_identity()

You should really think about if you want to use (simple) red and green in the same plot - ~8% of males can't tell the difference. Is there a good reason for colouring these bases but ignoring those people?

• 2 views • link
updated by Ram Ram • written by David W David W

whoops, hadn't noticed mmarchin's answer which is more or less the same as this, but with base graphics and is less hack-tastic :)

• 0 views • link
written by David W David W

Dear,

If you are working on proteins, you can use I-PV just as shown in the link here.

You will need to make your sequence file in a txt editor, ms excel etc. Here is an example.

You can visit the main website for more information.

I hope this helps,

Good luck with your research,

• 0 views • link
updated by Ram Ram • written by Ibrahim Tanyalcin Ibrahim Tanyalcin

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