I have done blastx of trinity assembled transcripts with nr database. I am not able to understand one thing from output results.
During blast alignment, sometimes query sequences start from beginning and subject sequence also in the same direction.
query start query end subject. start subject end 5 1000 8 350
but there are some cases also where one sequences direction is just opposite to the other sequence:
query start query end subject start subject end 5 850 250 2
please suggest why this kind of situation happen? are these both types of transcripts blastx correct?