Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

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.

share|improve this question
add comment

2 Answers

up vote 11 down vote accepted

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
share|improve this answer
    
Yeah, this is the standard answer. But note that BLAST works different with Protein. That's why it confused me for a while. –  ablmf Dec 16 '11 at 23:23
add comment

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.

share|improve this answer
    
I am afraid i don't understand what you are trying to say here. Could you please clarify? –  terdon Oct 8 '12 at 9:55
add comment

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.