This is an assignment that had confused me for a long time. So I think you guys who study computational biology might be interested. The original question is:

Find the two most similar DNA sequences of length 20 that Blast using a word length of 5 will fail to align.


2 Answers 2


BLAST works by finding a perfect match between sequences of a length equal to this "word length" and then enlarging it in a standard way -- yet there will be no alignment without this perfectly matched word.

So in your case, you must look for two 20bp sequences with no common 5bp sub-sequence; for instance:



  • $\begingroup$ Yeah, this is the standard answer. But note that BLAST works different with Protein. That's why it confused me for a while. $\endgroup$ Dec 16, 2011 at 23:23
  • $\begingroup$ Is "word length" == k-tuple? $\endgroup$
    – SmallChess
    Apr 15, 2015 at 5:56
  • $\begingroup$ @StudentT Precisely k in k-tuple. $\endgroup$
    – user59
    Apr 15, 2015 at 16:18

I am not sure I understand BLAST correctly.

When using BLAST in DNA and protein, they are different. There is a threshold T in protein "seeding" step, which means the seeding sequence is not perfectly matched. However, it seems there is no T in seeding step and we are looking for perfect match and extend them to neighbouring sequence.

So, if there is no word length 5 exact match between these 2 sequence, BLAST will fail.

  • $\begingroup$ I am afraid i don't understand what you are trying to say here. Could you please clarify? $\endgroup$
    – terdon
    Oct 8, 2012 at 9:55

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