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Promoter Seqs Summary

Jim Studier studier at ninja.life.uiuc.edu
Thu Feb 20 19:38:19 EST 1992

This is a summary of the promoter files I have collected so far.
It has Eukaryotic Promters but not Prokaryotic Promoters.
If more arrive I will sumarize again.

Dan Jacobson  (danj at jhuhyg.sph.jhu.edu) sent the following information about
   the Euk. Promoter Database. The '*'s are below the files I have looked at. 

Host fly.bio.indiana.edu

    Location: /molbio/data

	  FILE -rw-r--r--   94156 May 14  1991 euk-promoter.dat
          Description of each site in Database but no Sequences.

	  FILE -rw-r--r--   46615 May 14  1991 euk-promoter.doc

Host modl.unibas.ch

    Location: /biology/database
      DIRECTORY drwxr-xr-x        512  Sep 18 17:44  epd
    Location: /biology/database/epd
           FILE -rw-r--r--     240952  Dec 27 12:47  epd.dat
           FILE -rw-r--r--      49665  Dec 27 12:47  epduser.txt

Host ncbi.nlm.nih.gov

    Location: /repository/EPD/asn
           FILE -rw-r--r--    1154526  Aug 30 00:41  epd28.asn
           FILE -rw-r--r--     388444  Aug 30 00:39  epd28.bin
           FILE -rw-r--r--    1183577  Dec 17 16:07  epd29.asn
           FILE -rw-r--r--     398119  Dec 17 16:10  epd29.bin
    Location: /repository/EPD/db
           FILE -rw-r--r--     236892  Aug 22 17:46  epd28.dat
           FILE -rw-r--r--      49307  Aug 22 17:47  epd28.doc
           FILE -rw-r--r--     240950  Dec 17 16:13  epd29.dat
        *   Manual that describes database.  

           FILE -rw-r--r--      49664  Dec 17 16:13  epd29.doc
        *  Database that describes the complete sequences that
        *  the promoters came from.

        *  FILE -rw-r--r--     676489  Dec 17 16:05  epd29.seq
        *  This one contains actual promoter sequences.

    Location: /repository/EPD/ssa
           FILE -rw-r--r--      77657  Aug 30 01:44  epd28.chk
           FILE -rw-r--r--      79520  Dec 17 16:39  epd29.chk


This is the README file from Host :  ncbi.nlm.nih.gov 
                        Directory :  /repository/EDP/db
Contents of the EPD directory: 

Subdirectory db:

   - epd28.dat     EPD database release 28  
   - epd28.doc     EPD user manual release 28
   - epd29.dat     EPD database release 29
   - epd29.doc     EPD user manual release 29
   - epd29.seq     EPD release 29 sequence data in FASTA format

   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 sequence headers in epd29.seq are of the following

            >EPD17001 (+) Pv snRNA U1; range -499 to 100.

            The sequence identifier consists of the acronym EPD 
	    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 exhibiting the string "(+)" in the header

Subdirectory asn: 

   - epd28.asn     EPD release 28 in ASN.1 print value format  
   - epd28.bin     EPD release 28 in ASN.1 binary value format
   - epd29.asn     EPD release 29 in ASN.1 print value format  
   - epd29.bin     EPD release 29 in ASN.1 binary value format
   - asn.all       NCBI ASN.1 definitions 
   - EPDtoASN.f    FORTRAN program for epd.dat to epd.asn conversion 

   Notes:  - The ASN.1 version of EPD is not equivalent to the original 
	     EPD database. Certain types of information are missing. 
           - This EPD version is based on the general NCBI ASN.1 
	     definitions contained in file asn.all .

Subdirectory ssa:

   - SSASYSM.doc   SSA sequence-retrieval programs installation notes   
   - SSAUSRM.doc   SSA sequence-retrieval programs documentation
   - FromFPS.for   Main program FromFPS 
   - PRDSM.for     Main program PRDSM
   - RDBSQ.for     Subroutine RDBSQ
   - REMBL.for     Subroutine REMBL
   - STREV.for     Subroutine STREV

   - epd28.chk     Test output file for EPD release 28 (see SSASYSM.doc) 
   - epd29.chk     Test output file for EPD release 29 (see SSASYSM.doc) 

   Notes: These are the sequence retrieval programs mentioned in the EPD
	  user manual which run in a VAX/VMS/UWGCG environment. 

Philipp Bucher, December 17 1991


            Jim Studier  (studier at ninja.life.uiuc.edu)

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