lfk@eastman1.mit.edu (Lee F. Kolakowski) (01/23/91)
Organization: Mass. Inst. of Tech., Dept. of Chemistry Distribution: bionet Date: 23 Jan 91 10:59:02 Lines: 52 t, bairoch@cgecmu51.BITNET, bloom-beacon!rutgers!nwnexus.wa.com!farrah (Theresa Farrah), bryn@orchid.UCSC.EDU (Bryn Weiser - Bio. dept.), cmdsix@vaxa.weeg.uiowa.edu, compchem@gw.wmich.edu, cshort@NMSU.Edu, davison@uhnix2.uh.edu, gilbertd@silver.ucs.indiana.edu, gnu@toad.com, gwilliam@mrc-crc.ac.uk, jes@mbio.med.upenn.edu (Joe Smith), jkramer@umbio.miami.edu (Jack Kramer), kozar%CITIAGO.BITNET@mitvma.mit.edu (Lee G. Kozar), ljm@mayo.EDU (Larry Miller), macrakis@ri.osf.fr, model@ROCKY2.ROCKEFELLER.EDU, pauls @mrcvax.edinburgh.ac.uk, prasher@hyatt.whoi.edu (Doug Prasher), reisner@ee.su.oz.AU (Alex Reisner), roberts@CSHLAB.BITNET, rodrigol@ulrik.uio.no (Rodrigo Lopez), seqtest@wccf.mit.edu, templon@venus.iucf.indiana.edu (Jeffrey Templon), tobias@decpa.pa.dec.com, werner@helix.nih.gov (Werner Klee), wjb1@midway.uchicago.edu, prevelig.eastman1.mit.edu, atomeka@wccf.mit.edu 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 (128.91.18.14) 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@athena.mit.edu or lfk@eastman1.mit.edu or kolakowski@wccf.mit.edu| | Lee F. Kolakowski M.I.T. | | Dept of Chemistry Room 18-506 | | 77 Massachusetts Ave. Cambridge, MA 02139 | | AT&T: 1-617-253-1866 #include <disclaimer.h> | ======================================================================= ||Desert Storm - Lasers have made this the cleanest *dirty war* ever.|| =======================================================================
lonetto@psl.wisc.edu (04/30/91)
I'm writing to ask for help. I've been doing a sequence analysis project on a
group of related proteins. I have a set of 23 related sequences that I've been
able to align and now I want to do some analysis on the potential protein
structures involved. Does anyone out there have any code (preferably Pascal or
C) that will generate the "raw" data for structure prediction according to
Garnier et al. (JMB.120:97-120(1978))?? I need to get the numbers directly (NOT
the predictions) since I want to expand the analysis by taking the sequence
alignment into account. Basically, I want to average the values by position and
then subtract a penalty from the helix and beta-sheet scores for gaps in other
sequences at the position. I have a paper where a similar procedure was used
(Zvelebil et al. JMB.195:957-961(1987)). I have programs here that generate the
predictions, but as you can see, that doesn't do what I need. I have access to
unix, VMS and Macintosh in easy reach. If I have to I can borrow a DOS
machine. At present the "common" format my alignments are in is
intelligenetics, with .'s for gaps.
For that matter, does anyone have versions of standard programs (hydropathy,
hydrophobic moment, composition bias) adapted for use on multiple sequence
alignments?
Thanks,
Mike Lonetto lonetto@psl.wisc.edu (608)262-4620 / 262-4828