I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.
Version: 1.2.2.21.20090809-1 (blast2)
blast2 -p blastn -r 0 -q -2 -G 2 -E 2 -W 4 -e 0.1 -i queries.fasta -j target.fasta -o qt_blast.txt
When I use blast2 with individual queries (e.g. -i query_51.fasta) against the target the alignments work as expected (multiple HSPs per query). But if all the same query sequences are in one file (e.g. -i queries.fasta) I only get a just few alignment results (e.g. the last few queries).
Why is this happening and how can I use blast2 to perform a many-queries-to-single-target alignment?
Also, if I swap the files over, i.e. multiple small targets in one file and one large query:
blast2 -p blastn -r 0 -q -2 -G 2 -E 2 -W 4 -e 0.1 -i target.fasta -j queries.fasta -o qt_blast.txt
it gives different results again. In this case a single local alignment (the best HSP) for the (long) query to each (short) target. I'd be grateful if someone could explain why it is important which sequence is target and which query [with the blastn algorithm]. Cheers.