[Bioperl-l] DNA Sequencing two questions

[Jason Stajich]

For other fun picture games -- 

You can look at patterns of motifs/words in a chaos game representation of genomes.
http://mbe.oxfordjournals.org/content/16/10/1391.long
http://mbe.oxfordjournals.org/content/20/6/901.long


On Dec 7, 2011, at 1:59 PM, Smithies, Russell wrote:

> I did something similar a few years ago (after watching the movie "Contact" I think) and encoded codons as RGB values and drew an image of a genome. Looked much like random noise but I might try it again and draw as a space filling curve.
> I guess if you're looking for "hidden messages", why restrict yourself to 2 dimensions?  Perhaps something pops out as a single-image stereogram eg. http://upload.wikimedia.org/wikipedia/commons/8/8f/Stereogram_Tut_Random_Dot_Shark.png
> Perhaps it's a 3D "object" represented by slices drawn in a series of 2D planes?
> 
> But you need a bit of biological background as there will be patterns simply because of the way genes "work" and are laid out in chromosomes. You need to remember that DNA is effectively a 2D representation of a 3D protein structure and there is already much hidden information we know we don't understand - a "simple" task like how proteins fold is barely understood and why some become prions is still a mystery.
> 
> But don't let this stop you uncovering the great secret hidden in our genes :-)
> 
> On a similar note, have a look at http://medgadget.com/2011/10/send-your-secret-message-hidden-in-bacteria.html
> 
> --Russell
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of sunwukong
>> Sent: Thursday, 8 December 2011 8:05 a.m.
>> To: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] DNA Sequencing two questions
>> 
>> I am not a medical professional but I have two DNA related questions.
>> 
>> A year or so ago I realized that if the standard building blocks of life were the
>> amino acids GATC then they could be represented as a base 4 number
>> system (e.g., 0,1,2 and 3).  Then any life form could be represented by a
>> number (it would be very long).  So I set out on a quest to do this with a small
>> life form.  For fun I chose the Spanish Flu which I believe I found on an NIH
>> site.  Then I set out and realized that there was no standard.  And I did not
>> know if the number would be built with the most significant digit on the left
>> or right.
>> 
>> 1.  Is there a standard method for representing the ATCD molecules as
>> numbers g = 0 a = 1 t  = 2 c = 3
>> 
>> 2. is the sequence read left to right or right to left?
>> 
>> note:  It may be biologically significant if the right values are assigned to the
>> letters GATC, there could be a pattern somewhere that holds significant
>> information.  One idea might be to look at DNA sequences in bases other
>> than 4 to see if something jumps out.
>> 
>> http://www.insectscience.org/2.10/ref/fig5a.gif
>> 
>> VR
>> Pat Kirol
>> 509 442-2214
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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