[Biodevelopers] Blast not symmetrical?

[Michael Nuhn]

Hello, Everybody!

While I was trying to track down a "bug" in my program I found out that the
blast program (Blastn v2.2.11) is not symmetrical, that is:

If I blast a query sequence Q against a database S (1 sequence), I get a
result set B(S,Q).

If I do the blast the other way around, that is, I use S as query sequence
and blast it against the database Q, I get a result B(Q,S).

And the problem is: B(S,Q) and B(Q,S) are not equal. Each blast set has some
blast hits that the other does not have and also some blast hits that have
one common coordinate but end at another.

Both blasts were made with the blast defaults, no filter was used. The two
sequences are large (~2Mb each, the sequences are genomes). According to the
statistics used in blast (at least the part I understand), it should not
play a role which sequence is the query and which is the subject.

Does anyone have an explanation for this? Since I don't really have a clue
at where to start, hints and wild guesses are also appreciated.

Thanks in advance,
Michael.