1)
Three files (biosequence_schema.sql, est_ssr_schema.sql,
and RGP_Assembly_schemaDUMP.sql) contain the sql code to load a MySQL
server with 3 databases schemas.

Before loading these schemas you need to create these databases in 
MySQL.  The names of the DBs are:

        * biosequence
        This is an older version of bioperl's bioSQL schema.
        You should load it with the EST/unigene sequences using bioperl.

        * RGP_assembly
        See point 3) below.

        * est_ssr
        You should load it with SSR information (from Sputnik) and with
        similarity results after comparing EST/unigene sequences with the
        rice genome (using blast).

There is no particular reason why 3 separate databases.  I did this just
to simplify things for me.  If you wish to load all tables into a single
database, I suggest loading them into the est_ssr database and then modify
every perl script that talks to the database (modifications need to be done
deep in the code itself, but are simple to make, just a name change).

2)
The other 2 files included (ProcessBACoverlap_SSR.pl and
blast_result_HSP_rep_check.pl) are perl scripts to do some post processing of
data.  You must run these when the databases are loaded with est_ssrs and
sequences.

3)
The database RGP_Assembly contains the ordering of rice genome clones.  You
should probably load a more recent version.