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I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I give. Each of those aligned sequences have an e-value score representing the best hit by chance.

My question is how can I determine if the query sequence is highly conserved with the aligned sequence, or not? Can I determine that by saying the sequence with best hit e-value (lower e-value) is the one that is highly conserved? or are there other concepts that I need to consider in this case?

I appreciate your help!

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  • $\begingroup$ Whats the identity score like? $\endgroup$
    – Rover Eye
    Nov 21, 2015 at 21:21
  • $\begingroup$ The identity score is pretty consistent with the e-value score. I mean the higher the e-value score the higher the identity. I am curious what the "identity score" tells me about the aligned sequences. @RoverEye $\endgroup$
    – MEhsan
    Nov 21, 2015 at 23:33

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The "best" is the one with the highest ID score, lowest e-value and greatest length. There is no magic bullet, all of these are important. You should always look for the most similar sequence that matches as much as your query as possible with the lowest e-value possible.

Furthermore, it will depend on what you are looking at. If, for example, you are blasting a protein with a specific domain and are looking to find its homolog in another species, it is often more important that the domain be conserved than that the whole sequence be very identical. If you find a sequence with high identity but where the domain is not conserved, that is probably not what you are looking for.

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