Lee F. Kolakowski lfk at eastman1.mit.edu
Tue Jan 22 11:25:49 EST 1991

Organization: Mass. Inst. of Tech., Dept. of Chemistry
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Date: 23 Jan 91 10:59:02
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Subject: ProSearch Version 1.23 for Prosite 6.0

The scripts for Prosite Pattern Database Searching are now available 
for anonymous FTP from mbio.med.upenn.edu ( in 
/pub/ProSearch/*. There are several files for different machines.

	prosea12.zoo	- a zoo archive for MSDOS
	prosearch1.2.dclshar - a VMS shell script
	prosearch1.2.shar.Z - a Unix Shell archive compressed
	prosea12.uue	- a uuencode version of the zoo archive

New items included in ProSearch 1.2:
	cregex.c	-	a c program to generate the regex file
				written by Jack Leunissen.
	tfd2prosite	-	a c program to translate the TFD database
				to Prosite format by Ranier Fuchs.
	tfdsearch	-	Scripts similar to those in ProSearch for
				searching the TFD database.

It has become obvious that the same mechanisms used by ProSearch can
be extended to Nucleic Acids. Ranier Fuchs has now allowed the
extension of Prosearch Routines to search for Transcription Factor
recognition sites.  A forth coming extenstion will be other patterns
like restriction enzyme sites, proteolysis sites, and others.

In order to implement tfdsearch the file sites.dat from ncbi.nlm.nih.gov
was required. Thes is the pattern file from David Ghosh's TFD database.

I hope you all continue to use Prosearch with useful results.

Future releases will only occur if there are new capablities added.
cregex.c will allow you to update you regex files upon new database
release without my intervention.


Frank Kolakowski

|lfk at athena.mit.edu or lfk at eastman1.mit.edu or kolakowski at wccf.mit.edu|
| Lee F. Kolakowski                 M.I.T.                            |
| Dept of Chemistry                 Room 18-506                       |
| 77 Massachusetts Ave.             Cambridge, MA 02139               |
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