Q: Does it matter which sequence is used as the "reference" (given to
   lastdb) and which is used as the "query" (given to lastal)?

A: It may do.  In short, LAST tries hard to find alignments for every
   position in the query.  When mapping reads to a genome, you
   probably want the genome to be the reference, and the reads to be
   the query.  That way, for each read, it will search for several
   most-similar locations in the genome.  The other way, for each
   location in the genome, it will search for several most-similar
   reads.  As another example, if you compare a genome to a library of
   repeat sequences, you probably want the genome to be the query and
   the repeat library to be the reference.


Q: Why is LAST so slow at reading/writing files?

A: Probably because the files are huge and your disk is slow (or lots
   of people are using it).  Try to use a reasonably fast disk.


Q: How can I find alignments with > 95% identity?

A: One way is to use a scoring scheme like this: +5 for a match, and
   -95 for a mismatch or a gap.  You'll also need to set the alignment
   score threshold to a reasonable value.  In this example we set it
   to 150, which means that we require at least 30 matches:

     lastal -r5 -q95 -a0 -b95 -e150
