[Bioperl-l] DNA Sequencing two questions

[Smithies, Russell]

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
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================