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I'm taking an online bioinformatics class and I am stuck on a problem. The resources I have found don't help that much. Here is the problem:

"Assemble the error-free reads from a circular genome on the dataset below. You do not need to consider the reverse complement of the reads.

Dataset: CGTTCT CTAG GACGT TAGAC

As the reads do not have the same length, convert the reads to 4-mers using the approach proposed by Idury and Waterman."

I believe this means I need to convert this into sets of 4 characters each. Do I simply break them up by taking the first 4 characters and last 4 characters like this?

CGTTCT: CGTT --> TTCT
CTAG: CTAG --> CTAG
GACGT: GACG --> ACGT
TAGAC: TAGA --> AGAC

And end up with a new dataset of: "CGTT TTCT CTAG GACG ACGT TAGA AGAC"?

Or is there more to it than that? Thanks for any help.

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    $\begingroup$ I would guess that it would be all 4mers. In this case that would mean that CGTTCT would also yield GTTC. But as I say - this is a guess. $\endgroup$
    – Alan Boyd
    Feb 21, 2014 at 6:05
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    $\begingroup$ It does in fact mean all possible 4mers. I don't know how much material you get from the course, but they refer to this paper: citeseerx.ist.psu.edu/viewdoc/… $\endgroup$
    – skymningen
    Feb 21, 2014 at 7:12
  • $\begingroup$ To be sure I'm understanding correctly, does that mean the new dataset should be: "CGTT GTTC TTCT CTAG GACG ACGT TAGA AGAC"? $\endgroup$
    – Bryan
    Feb 21, 2014 at 21:19

1 Answer 1

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Actually the new data set will be,

for k = 4 (k-mer value)

CGTTCT -> CGTT GTTC TTCT

or

enter image description here

Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/

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