How to Determine the Most Conserved Sequence from BLAST Result?

Question

[Bahrani]

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!

Answer 1

[Michael]

"how can I determine if the query sequence is highly conserved with the aligned sequence".

This is a misconception of the term sequence conservation. Sequence conservation is a property of multiple homologous sequences, or a clade of sequences in a phylogeny, under evolution from ancestral sequences. For this reason, conservation cannot be determined from comparing only two sequences. There is no such thing as mutual conservation of two sequences. Two sequences have transitive sequence similarity, it obviously makes no sense to ask, if sequence A is more similar to B than B to A. Evidence for sequence conservation can be determined from multiple alignments of homologs and by looking at orthologs from many divergent taxa. See https://en.wikipedia.org/wiki/Conserved_sequence