README for PairsDB 2/2009
March 9th 2010.

This PairsDB update was created using sequence
data that was collected form UniProt, RefSeq and PDB
databases on September 14th 2009.


PairsDB ftp site content

The PairsDB database contains several dozens of MySQL tables. 
Two different distribution formats are used in the tables in this ftp site. 


1. LARGE TABLES

The two largest tables, pairsdb_90x90 and psiblast_40x40, are split into several  
tab delimited text files. To install these tables  you must first create a set of empty tables 
with the corresponding SQL command file ( pairsdb_90x90.sql or psiblast_40x40.sql)

This can be done with commands like:

   mysql --local -u username --password password pairsdb < pairsdb_90x90.sql

After this you can unzip the data files and feed in the data files using mysqlimport command. 
For example:

   foreach number ( 1 2 3 4 5 6 7 8 9 10 11 )
      gunzip "pairsdb_90x90_"$number"M.table.gz"
      mysqlimport --local --compress -u username --password password \
      pairsdb  "pairsdb_90x90_"$number"M.table"
      # rm -f pairsdb_90x90.$number.table # if you wish to free some disk space
   end

Note that the SQL commands used to create tables will cerate indexes for the query_nid column. 


2. OTHER TABLES

All the other pairsd-tables are distributed as MySQL dump files. 
To read this data to the database, just unzip the files and feed them to 
MySQL-client. For example:

   gunzip nrdb.dump.gz
   mysql --local -u username --password password pairsdb < nrdb.dump


Please see http://pairsdb.csc.fi/ for more information.