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A Genome Puzzle


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4 replies to this topic

#1 superprismatic

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Posted 25 May 2013 - 06:08 PM

In sequencing DNA, technicians break up long molecules into
smaller pieces because it is easier to sequence small segments
than long ones. They must then reconstruct the target molecule
by fitting the small segments together using overlaps as a guide.
The small segments are sequenced beginning at either end in a
random fashion. So, for example, the segment ATACAG may also
be sequenced as GACATA.

In this puzzle, I have chopped up many identical 50-long sequences
into pieces of lengths 5, 6, 7, and 8. 30 of these pieces are:

ATACAG
TGACAT
GTCTTA
GTCGAGA
AACGA
CAAGG
CAGTGTGA
GTGGTGT
CCGATGAC
AGACAA
TGTGA
ATACAGTG
CTGTG
ACATA
GTGTCG
TACAGT
GTCTTAG
CATAA
GGTGG
GACTCCAG
TGTGA
CCAGTG
TGTGACA
GTGACATA
TGTGGT
ATTCTGA
TGAATACA
TAGCCG
TGTGACCT
CCTCA

I have insured that these 30 pieces completely cover the 50-long
sequence with which I started. Can you find that sequence?
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#2 bonanova

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Posted 31 May 2013 - 07:40 PM

I like this.
A one dimensional jigsaw puzzle.
I'll give it a look this weekend.
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The greatest challenge to any thinker is stating the problem in a way that will allow a solution.
- Bertrand Russell

#3 bonanova

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Posted 07 June 2013 - 05:20 PM

I gave it a try.  Too many options to sort out. That is to say I could not program it.


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The greatest challenge to any thinker is stating the problem in a way that will allow a solution.
- Bertrand Russell

#4 harey

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Posted 08 October 2013 - 05:17 PM

Still unsolved... I tried to omit chunks that are contained in other chunks (i.e. TGTGA is there twice and is contained in TGTGACA). I hoped that with the reminder I would be able to build longer chunks. Still too many combinations.

 

How is it done in praxis?


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#5 plasmid

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Posted 10 October 2013 - 03:13 PM

Biologists don't tackle the question quite like it was posed in the OP.

If you read a DNA sequence like ATATCAGG, the read in the opposite direction wouldn't be GGACTATA. Nucleotides have a directionality; the "preceding" nucelotide would be attached to the 5' carbon of the nucleotide you're looking at, and the "following" nucleotide would be attached to the 3' carbon, and all (or nearly all) of our techniques start from the 5' end and work toward the 3' end. So this would look unambiguously like 5'-ATATCAGG-3'.

The tricky part is that DNA is double stranded, where each A is paired to a T on the opposite strand and each C to a G. And the strands run in opposite directions. So for the above sequence, you would have the two strands

5'-ATATCAGG-3'
...||||||||...
3'-TATAGTCC-5'


If you turn the complementary strand to show it in the conventional 5' to 3' orientation it would be 5'-CCTGATAT-3'. And there's generally no way to tell if you're looking at the strand of interest or its complementary strand.


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