22-Jan-2014

fasta36/sql

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Perl and SQL for creating and searching mySQL and pgSQL sequence
databases.

See A. J. Mackey and W. R. Pearson (2004) "Using SQL databases for
sequence similarity searching and analysis" Current Protocols in
Bioinformatics L. Stein, Ed. Wiley, New York, pp 9.4.1-9.4.25

create_seq_demo.sql
mysql_demo1.sql   -- SQL file for fasta36 format 16 to search seqdb_demo databse
mysql_demo_pv.sql -- SQL file for searching 50000 Swissprot sequences using database format 16 (mysql)
		     fasta36 ../seq/mgstm1.aa "../sql/myql_demo_pv.sql 16"
nr_to_sql.pl	  -- perl script to create mysql seqdb_demo sequence database
pirpsd.sql        -- SQL file for fasta36 format 16 to search custom PIR database (obsolete)
psql_demo1.sql    -- pgSQL version of mysql_demo1.sql
psql_demo_pv.sql  -- pgSQL version of mysql_demo_pv.sql

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alternate expansion strategy

join_up50.pl      -- more sophisticated way to generate expanded sequences using SQL