[Bioperl-l] DNA Sequencing two questions

[Smithies, Russell]

I tried again and came up with this:
http://www.bioperl.org/w/images/7/7a/Autostereogram.png
If you look carefully, you can see the answer to life, the universe, and everything!!

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> Sent: Thursday, 8 December 2011 10:59 a.m.
> To: 'sunwukong'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] DNA Sequencing two questions
> 
> 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_Ra
> ndom_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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