When does BLAST fail to align 2 DNA sequences?

Question

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.

score 13 · Accepted Answer · 2011-12-16T20:29:03.863

13

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:

AAAAAAAAAAAAAAAAAAAA

and

AAAACAAAACAAAACAAAAC

edited Dec 16 '11 at 20:29

answered Dec 16 '11 at 19:56

Yeah, this is the standard answer. But note that BLAST works different with Protein. That's why it confused me for a while. – NonalcoholicBeer Dec 16 '11 at 23:23
Is "word length" == k-tuple? – SmallChess Apr 15 '15 at 05:56
@StudentT Precisely k in k-tuple. – Apr 15 '15 at 16:18

score -1 · Answer 2 · edited Oct 07 '12 at 23:29

-1

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.

edited Oct 07 '12 at 23:29

jonsca

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answered Oct 07 '12 at 21:18

user1503

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I am afraid i don't understand what you are trying to say here. Could you please clarify? – terdon Oct 08 '12 at 09:55

When does BLAST fail to align 2 DNA sequences?

2 Answers2