what is the explanation when we find 100% of similarity between two speicies in the blast test then we find 57.5 % of pairwise distance between the same two spicies??
The similarity in BLAST is limited to the portions that overlap. So two sequences need not necessarily be identical over their full length in order to obtain a high similarity score.
What do you exactly mean by distance? How was it calculated?
thank you for the answer, actually I am not specialist in molicular biology but I need to discuss my DNA barcoding resuts (working on an inventory), the distance that I calculated is the P_distance, I calculat it with MEGA.software I saw many articals use this distance but I could not understande the aim. actually I whant to know if the blast results are suficient to say that COI barcodes is adicuate to seperate and identify the sampled species.
As was mentioned, BLAST uses local alignment. In contrast, the p-distance in MEGA is literally just a proportion of bases (globally between the two) that are different.
So your results mean that although the two sequences are different at 57% of bases, they are 100% identical for a particular subsequence. Take a look at your BLAST results and see how much/ where they actually align.
[BLAST] compare des morceaux (la similitude entre des fractions de votre séquence à d'autres fractions dans d'autres séquences dans la banque)... La distance [MEGA] sert à construire les arbres des liaisons phylogénétiques (toute la première séquence est comparée à toute la deuxième séquence à la fois). j'espère que ça réponds à votre question.
Yes the query coverage is the percentage of bases that the query aligned to the match sequence, and the identity describes their similarity over just those bases (not over the entire sequences). Scroll further down your BLAST results (assuming you are using the NCBI web interface) and you should be able to view the actual alignment. This might help.
Tyler Chafin thank you I understand know what is query coverage and yes I use NCBI or this case identy was 100% and query coverage was 100% so how can this happen
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