Q: Does it matter which way round you do the alignment: e.g. cat
versus mouse, or mouse versus cat?

A: The results may be different.  When comparing two similar-sized
genomes, the difference should be minor.  When mapping tags to a
genome, you probably want the genome to be the database, and the tags
to be the query.  That way, for each tag, 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 tags,
which is probably not what you want.  As a final 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 database.


Q: Why does lastdb run forever without finishing?!

A: Perhaps you gave it two copies of the same genome by mistake?  It
becomes horribly slow if there are huge exact repeats.  (But it copes
OK with the exact duplicates between chromosomes X and Y in some
versions of the human genome.)
