Difference when inverting query and subject in Blastn

Question

[ailtonpcf]

I have a given output Blasting short sequences (microRNAs) as query and a microRNA-seq as subject. When I set up short sequences (microRNAs) as subject and a microRNA-seq as query, in other words, inverting the inputs, I have different results. Can anyone help me understand what happens? I am not sure, but I guess have read in any post anyone talking about the size of the database.

[Lucila]

Hi! This post was useful to me when I had a similar doubt. I hope it helps.

https://edwards.sdsu.edu/research/is-there-a-difference-between-a-query-to-db-blast-and-a-db-to-query-blast/

[ailtonpcf]

Thank you Lucila, it helped !

Answer 1

[lieven.sterck]

Blast results are not symmetrical, meaning that blasting A to B will not necessarily produce the same result (score etc) as blasting B to A . This is a common misconception. One of the (most important) factors is indeed, as you mentioned, the blastDB size (you can 'resolve' that partially by using a fix DB size, cfr the blast manual for the syntax) and will mainly influence the E-vlaues score. The bitscore is more directly related to the actual alignment and will thus not differ (if at all) as much as the e-value.