Contents of the EPD directory:

Subdirectory XXX (indicating EPD release number):

   - epdXXX.dat      EPD database release XXX
   - epdXXX.idx      index of epdXXX.dat based on AC and ID
   - epdXXX.usr      EPD user manual for release XXX
   - epdXXX_bulk.dat bulk EPD database release XXX
   - epdXXX_bulk.idx index of epdXXX_bulk.dat based on AC and ID

Subdirectory current: always the latest release

   - epd.dat                 EPD database
   - epd.idx                 index of epd.dat based on AC and ID 
   - epd.seq                 EPD promoter sequences in FASTA format
   - epd.usr                 EPD user manual
   - epd_bulk.dat            bulk section of EPD database
   - epd_bulk.idx            index of epd_bulk.dat based on AC and ID 
   - epd_bulk.seq            sequence data in FASTA format of bulk section of EPD
   - epd_16K.seq             EPD release XXX sequence data in FASTA format
   - epd_16K_seq.idx         epdXXX_16K.seq index based on AC
   - epd_bulk_16K.seq        sequence data in FASTA format of bulk section of EPD release XXX
   - epd_bulk_16K_seq.idx    epdXXX_bulk_16K.seq index based on AC

   Notes:  - The original EPD format defines promoter sequences
             indirectly by pointers to EMBL sequence data. These 
             pointers are only correct for EPD and EMBL versions  
             of the same release. 

           - The files epd.seq and epd_bulk.seq contain sequence data for
             EPD promoter entries in the range -499 to +100 relative to the
             transcription initiation sites. Instead, the files epd_16K.seq and
             epd_bulk_16K.seq contain sequences in the interval -9999 to 6000
             relative to transcription initiation site.
  
Subdirectories SRS6 (no longer maintained!): 
 
   - epd.i          it describes the logical stucture of the database 
   - epd.is         it describes the syntax of the database entries
   - epd.it         it is the description of the database served by the
                    SRS www server 
   
Subdirectories views:

   - epd_for_integr8.xml	current EPD release XXX in XML format provided 
                                for integr8 project at EBI
   - epdXXX.xml			EPD release XXX in XML format
   - epdXXX_xml.idx		epdXXX.xml index based on AC
   - epd.dtd			EPD DTD file for XML format
   - epd.xsl			associated stylesheet for XML format
   - epdXXX.seq			EPD release XXX sequence data in FASTA format
   - epdXXX_seq.idx		epdXXX.seq index based on AC	
   - epdXXX_bulk.seq		sequence data in FASTA format of bulk section of EPD release XXX
   - epdXXX_bulk_seq.idx	epdXXX_bulk.seq index based on AC	
   - epdXXX_16K.seq             EPD release XXX sequence data in FASTA format
   - epdXXX_16K_seq.idx         epdXXX_16K.seq index based on AC  
   - epdXXX_bulk_16K.seq        sequence data in FASTA format of bulk section of EPD release XXX
   - epdXXX_bulk_16K_seq.idx    epdXXX_bulk_16K.seq index based on AC
   - epd-emblXXX.dr		List of all EMBL accession numbers and their 
                                corresponding EPD ACs and IDs
   - README			this file
 
  

   Notes:  - All sequence data files in this directory have been automatically
             compiled from the EMBL release XXX division files using the 
             sequence position pointers in EPD.  
 
           - The files epdXXX.seq and epdXXX_bulk.seq contain sequence data for
             EPD promoter entries in the range -499 to +100 relative to the
             transcription initiation sites. Instead the files epdXXX_16K.seq and
             epdXXX_bulk_16K.seq contain sequences in the interval -9999 to 6000
             relative to transcription initiation site.

           - The sequence headers in epdXXX.seq and epdXXX_bulk.seq are of the
             following type:

             >EP17001 (+) Pv snRNA U1; range -499 to 100.

             The sequence identifier consists of the acronym EP 
             followed by the corresponding EPD entry code. The
             plus sign in parentheses reflects the "independent
             subset status" as described in the EPD user manual.
             For statistical analysis, it is recommended to use only 
             those sequences containing the string "(+)" in the header
             line.

4 May 2011
EPD developers