[bionet.molbio.embldatabank] Eukaryotic cis-acting transcription regulatory elements

<BACKD@QUCDN.QueensU.CA> (02/05/91)

Is there a database of consensus transcription factor recognition sequences
that can be used to scan a promoter sequence? I find running a promoter
sequence against the entire database at low enough "stringency" to
identify short regulatory elements generates a very large number of
irrelevent matches. If not, are there any moves to compiling and maintaining
such a database?

<BACKD@QUCDN.QueensU.CA> (02/07/91)

Thanks to all of those who responded to my request.
This is a brief summary of my E-mail on the subject:

- David Gosh (Nucl. Acids Res. 18, 1749-1756) has developed a relational
 database of transcription factor recognition elements called TFD. The
 TFD database can be obtained in one of two ways:
   1. Anonymous FTP from NCBI.NLM.NIH.GOV in /repository/TFD
   2. From EMBL mailer. Send a message to the mailer as follows
      Address: NETSERVER@EMBL.BITNET
               HELP
               HELP TFD
               DIR TFD
     The mailer will return the appropriate help files to get you started.

- Dan Prestridge from Los Alamos Nat'l Labs writes that he has a program,
  SIGNAL SCAN available in MS-DOS or UNIX format that will scan a sequence
  file against the TFD database. The database is included on the disk.
  Mail Dan a request for either format at DXP%LIFE@LANL.GOV. The UNIX
  version can be E-mailed back, the MS-DOS version travels better on a
  diskette, so be prepared to send along two formatted discs.

- Those operating in the UNIX world have a third option.
  MBCRR.Harvard.Edu have a UNIX program called DYNAMIC that used the TFD
  database directly. D. Gosh refers to the program in his NAR paper.

 -Be aware the TFD database is about 500K.

 -Good luck and thanks for all the help.

Don Back, BACKD@QUCDN.QueensU.CA.BITNET
(613) 545-2982