What is the GrailEXP Database Format (GXPDF)?
A database my.db is said to be in GrailEXP Database Format (GXPDF) if the following conditions are true: • The file my.db contains only FASTA sequences. • Each FASTA header is pipe-delimited and of the form >organism|accession number|database|……, where organism is the tag for that organism (i.e. human, mouse, arab, droso) obtained from doing grailexp –listorgs. • The database is blastable, i.e. my.db.nhr, my.db.nin, and my.db.nsq all exist. • A valid GrailEXP index file my.db.gxp exists. The database has to be in FASTA format, with the proper headers, and be formatdb’ed for use with BLAST and indexed for use with the Galahad alignment program. Thus the steps to building a database in GXPDF are: • Build the database, altering the headers as necessary to put the organism in the first field, the accession number in the second field, and a database tag in the third field. • (Optional) Partition the database into multiple files. • Formatdb the database(s) for use with BLAST. • Index th
