---------------------------------------------------------------------------- ************************************* * Programs that make use of PROSITE * ************************************* Name : PROSITE.PRG Topic : Describes the programs (academic or commercial) that make use of the PROSITE database. Also includes a section on email servers Last revised: February, 1995. ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- 1) PUBLIC DOMAIN PROGRAMS ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Program : MacPattern Author : Rainer Fuchs Address : Glaxo Research Institute 5 Moore Drive Research Triangle Park, NC 27709 USA Telephone: +1-919-9904434 FAX : +1-919-9900026 Email : rf11522@glaxo.com Runs on : Apple MacIntosh; System 6.0.5 or greater, MultiFinder compatible. Version : 3.1 of September 1993. Citation : Fuchs R. MacPattern: protein pattern searching on the Apple MacIntosh. Comput. Appl. Biosci. 7:105-106(1991). Fuchs R. Predicting protein function: a versatile tool for the Apple MacIntosh. Comput. Appl. Biosci. 10:171-178(1994). Availability: Available from the EBI File Server. Send a message to the following address: netserv@ebi.ac.uk, the message should contain the following line: GET MAC_SOFTWARE:MACPATTERN.HQX You will receive back by email a file containing MacPattern, once you have transferred it to you Mac you must decode it by (Un)StuffIt. Also available by anonymous ftp from "ftp.ebi.ac.uk", the program can be found in "/pub/software/mac/macpattern.hqx" Description : MacPattern allows you to use PROSITE (or any pattern database adhering to the PROSITE conventions) for searching protein (or DNA) sequences for the occurence of known patterns. You may search for all patterns in the database, for selected entries or you may create "patterns sets". The complete documentation for each pattern in Prosite can be accessed easily. Output can be viewed on screen, printed, saved to disk or copied to the Clipboard. MacPattern accepts to read protein sequences in the following formats: SWISS-PROT, NBRF/PIR, Pearson's FASTA, Intelligenetics, DNA-Strider, DNAid, and ASCII. Works with individual sequences or sets of sequences, including SWISS-PROT on the EMBL CD-ROM. Version 2.0 and later also utilise Henikoff's BLOCKS database for searches of protein sequences with site-specific scoring matrices. Output is evaluated according to the "strength" value provided in each database entry. Another option is the identification of statistically significant protein segments using the Maximal Segment Score method by Karlin and Altschul. ---------------------------------------------------------------------------- Program : EMBL-Search Author : Rainer Fuchs Address : Glaxo Research Institute 5 Moore Drive Research Triangle Park, NC 27709 USA Telephone: +1-919-9904434 FAX : +1-919-9900026 Email : rf11522@glaxo.com Runs on : Apple MacIntosh; System 7 "friendly", MultiFinder compatible. For use with the EMBL Sequence Databases CD-ROM. Version : 2.4 of September 1993. Citation : Fuchs R., Stoehr P. EMBL-Search - A CD-ROM based database query system Comput. Appl. Biosci. 9:71-77(1993). Availability: Available from the EBI File Server. Send a message to the following address: netserv@ebi.ac.uk, the message should contain the following line: GET MAC_SOFTWARE:EMBL-SEARCH.HQX You will receive back by email a file containing EMBL-Search once you have transferred it to you Mac you must decode it by (Un)StuffIt. Also available by anonymous ftp from "ftp.ebi.ac.uk", the program can be found in "/pub/software/mac/embl-search.hqx" Also distributed with the EMBL CD-ROM releases. Description : EMBL-Search is a free database query and retrieval program for the Apple MacIntosh for use with the EMBL Sequence Databases CD-ROM. Allows text queries of the PROSITE protein pattern database, in addition to the EMBL nucleotide and SWISS-PROT protein sequence databases. Cross-references between EMBL, SWISS-PROT, PROSITE (data), and PROSITE (doc) can be used to navigate easily between these databases. ---------------------------------------------------------------------------- Program : PATTERN Author : Olivier Boulot Address : Genethon 13, place de Rungis 75013 Paris France Telephone: +33-1-45651300 Email : lydie@mpi.com Runs on : Unix Language : C (code is available). Version : 1.0 of January 1991. Citation : None (if necessary cite as unpublished method). Availability: Send an email message to the author. Description : PATTERN will scan a sequence or a protein sequence database with the patterns stored in PROSITE. It entirely supports the PROSITE syntaxe. Can also work on nucleotides. ---------------------------------------------------------------------------- Programs : PIP, SPLITP1, SPLITP2, SPLITP3. Author : Rodger Staden Address : MRC Laboratory of Molecular Biology Hills Road Cambridge, CB2 2QH United Kingdom Telephone: +44-223-248011 Email : rs@mrc-lmb.cam.ac.uk Runs on : VAX with VMS or Ultrix DEC Alpha (OSF 1) Unix (Sun OS; Solaris; IRIX; etc.) Citation : Staden R. Screening protein and nucleic acid sequences against libraries of patterns. DNA Sequence 1:369-374(1991). Availability: Send an email message to the author. Description : PIP can screen protein sequences against the whole PROSITE database or against a specific pattern entry in PROSITE. SPLITP1: splits the file PROSITE.DAT so that there is a separate file for each entry. Each file is automatically named "psentry-number.dat" (example PS00197.DAT). In addition an index file is created. SPLITP2: splits the file PROSITE.DOC so that there is a separate file for each document entry. Each file is automatically named "pdocentry-number.doc" (example PDOC00128. DOC). SPLITP3: intereprets the PROSITE.DAT file and rewrites it in a notation speicific for the PIP program. This utility produces various files. ---------------------------------------------------------------------------- Program : PPS Author : Wang Huaichun Address : Department of Biotechnology Information Service Institute of Medical Information 27 Taiping Road Beijing 100850 China Telephone: +86-1-8214640 FAX : +86-1-8213044 Citation : Wang H., He Y. PPS: A computer program for searching protein motifs based on the PROSITE database. China High Tech. Lett. 4:30-33(1994). Runs on : MS-DOS Language : C Version : 1.0 Availability: Available in China from the author. Description : Program to search protein sequences for the occurrence of PROSITE patterns. ---------------------------------------------------------------------------- Program : ProSearch Author : Lee F. Kolakowski Jr. Address : Massachusetts General Hospital Renal Unit Charlestown Navy Yard / Building 149 13th Street Boston, MA 02129 USA Telephone: +1-617-7265666 FAX : +1-617-7265669 Email : lfk@receptor.mgh.harvard.edu Runs on : Any system with a complete implementation of AWK programming language. Is known to run on Unix platforms, VAX VMS, MS-DOS. Language : AWK Version : 2.1 of September 1992 Citation : Kolakowski L.F. Jr., Leunissen J.A.M., Smith J.E. ProSearch: fast searching of protein sequences with regular expression patterns related to protein structure and function. Biotechniques 13:919-921(1992). Availability: Available from the EBI File Server. Send a message to the following address: netserv@ebi.ac.uk, the message should contain one of the following three lines: GET UNIX_SOFTWARE:PROSEARCH.UAA GET VAX_SOFTWARE:PROSEARCH.UAA GET DOS_SOFTWARE:PROSEARCH.UAA You will then receive back by email the file containing a shell archive of ProSearch. Non-Unix version will be packaged in ZOO archives or as VMS DCL_Shell archives. Description : ProSearch allows direct searching of regular expressions on protein sequences. The PROSITE patterns must be translated into Unix-style regular expressions by hand or by cregex (see the description for that program). One or more protein sequences can be swiftly searched for all patterns in the database. Patterns can be easily developed and added to the database. All output is written to standard output, and as such can be redirected to any device. The input format is constrained to just sequence, but many input formats can be handled by filtering the input through READSEQ (gilbert@iubio. vax.indiana.edu). There are two levels of output. The simplest is a table of sites in the protein which match patterns in the database, and the pattern's name. The more complete output is this table, the sequence matched, and the PROSITE documentation associated with the pattern. ---------------------------------------------------------------------------- Program : cregex Author : Jack A.M. Leunissen Address : CAOS/CAMM Center University of Nijmegen Toernooiveld 6525 ED Nijmegen The Netherlands Telephone: +31-80-652248 Email : jackl@caos.caos.kun.nl Runs on : VAX with VMS, Unix, MS-DOS Language : C (code is available). Version : 1.2 of September 1992 Citation : None (if necessary cite as unpublished method). Availability: Available from the EBI File Server. Send a message to the following address: netserv@ebi.ac.uk, the message should contain one of the following three lines: GET UNIX_SOFTWARE:CREGEX.C GET VAX_SOFTWARE:CREGEX.C GET DOS_SOFTWARE:CREGEX.C You will receive back by email a file containing cregex.c Description : cregex reformats the native PROSITE database into a file containing regular expressions, which can be used in the pattern matching language AWK. Entries containing a range are split into multiple patterns. The regular expression file is most conveniently used in combination with PROSEARCH scripts (see the description for that program). ---------------------------------------------------------------------------- Program : prosite Author : Klaus Hartmuth Address : Institut fuer Biochemie University of Vienna Waehringerstrasse 17 A-1090 Vienna Austria Telephone: +43-222-436141-56 Email : a5161dad@awiuni11.bitnet a5161dad@vm.univie.ac.at Manfred D. Zorn (for the UNIX version) Address : Human Genome Center MS 50B-3238 Lawrence Berkeley Laboratory 1 Cyclotron Road Berkeley, CA 94720 USA Telephone: +1-510-4865041 Email : mdzorn@lbl.bitnet mdzorn@lbl.gov Runs on : IBM 3090 mainframe under VM/CMS Unix Language : C (code is available). Version : 1.2 of October 1991. Citation : None. Availability: VM/CMS version: send an email message to the author UNIX version: by anonymous ftp from "genome.lbl.gov"; the file to get (in binary mode) is: ProSite.shar.Z and is located in the directory "/pub/prosite". Description : Scans a given protein sequence for the occurrence of any pattern listed in PROSITE. Input files in SWISS-PROT, FASTA or plain ASCII formats are recognized. The program output can be saved in an ASCII file and shows the position of the patterns under the sequence, as well as the complete PROSITE pattern. Program flags can be set to exclude the PROSITE.DOC or to include the PROSITE.DAT information. A position table of pattern occurences is produced for each pattern. A complete list of flags is obtained by calling the program with the -h flag, as shown here: usage: prosite -hixvrqst -w -p [in.file] [out.file] -h help -i include PROSITE.DAT info -x exclude PROSITE.DOC info -v show program version -r show library release -q keep quiet -s suppress output -t create prosite.tbl supply target disk as optional argument (CMS only) -w aa/line in output -p pattern size to ingnore ---------------------------------------------------------------------------- Program : Scrutineer Authors : Peter R. Sibbald, Hubert Sommerfeldt, and Patrick Argos Address : EMBL Data Library PostFach 10.2209 D-69012 Heidelberg Germany Telephone: +49-6221-387491 Email : sibbald@EMBL-Heidelberg.DE Runs on : VAX with VMS Unix Language : Pascal (code is available). Version : June 1992. Citation : Sibbald P.R., Argos P. Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequence databases. Comput. Appl. Biosci. 6:279-288(1990). Sibbald P.R., Sommerfeldt H., Argos P. Automated protein sequence pattern handling and PROSITE searching. Comput. Appl. Biosci. 7:535-536(1991). Availability: Available from the EBI File Server. Send a message to the following address: netserv@ebi.ac.uk, the message should contain the following line: GET VAX_SOFTWARE:SCRUTINE.UAA You will then receive by email the program split into 9 parts; you must then UUDECODE these files using the UUD program and uncompress the resulting file using the ZOO program. If you do not have the UUD or ZOO programs or if the above description seems cryptic to you, then you should first send the following message to netserv@ebi.ac.uk: HELP VAX_SOFTWARE Also available by anonymous ftp from "ftp.ebi.ac.uk", the program can be found in "/pub/software/vax/scrutine.uaa". Description : Scrutineer is a program designed for searching protein sequences for patterns, motifs, alignments and so on. A very wide range of patterns can be handled. One option in Scrutineer is to place patterns in a file and then search typically a small number of sequences for all patterns. We provide PROSITE patterns in Scrutineer format in a file. A new protein sequence can be readily searched for all PROSITE patterns. The interface to the program is simple and command driven. The code is portable. The user may easily generate their own patterns for later use. Scrutineer does NOT make use of the documentation associated with each PROSITE pattern (to tour the documentation we use routines like VAX SEARCH or Unix grep instead). A manual comes with the program. ---------------------------------------------------------------------------- Program : PROTOMAT Authors : Jorja Henikoff and Steven Henikoff Address : Howard Hughes Medical Institute Fred Hutchinson Cancer Research Center 1124 Columbia Street, M-684 Seattle, WA 98104 USA Telephone: +1-206-6674515 Email : henikoff@sparky.fhcrc.org Runs on : IBM PC compatible systems; DOS 3.1 and higher SUN (Sparc) with SunOS Version 4 Version : 5.0 of June 1992 Citation : Henikoff S., Henikoff J. Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19:6565-6572(1991). Availability: Both MS-DOS and Unix versions are available by anonymous ftp from ncbi.nlm.nih.gov. The files to get (in binary mode) are: A) For DOS: In the "/repository/blocks/protomat.dos" directory. You should get all the files in that directory. B) For Unix: In the "/repository/blocks/protomat.unix" directory. You should get: README.protomat protomat.tar.Z You should then, once the files are transferred: uncompress protomat.tar.Z tar -xvf protomat.tar cd protomat make protomat Description : Reads an entry from PROSITE.DAT and extracts all true positive and false negative sequences listed there from SWISS-PROT. Runs H.O. Smith's "motif" algorithm (PNAS 87:826-830) on the group of proteins and extends the motifs into blocks. Assembles a "best path" set of blocks describing the group of proteins. ---------------------------------------------------------------------------- Program : PATMAT Author : James C. Wallace Address : Fred Hutchinson Cancer Research Center 1124 Columbia Street Seattle, WA 98104 USA Telephone: +1-206-6674501 Email : root@fred.fhcrc.org Runs on : IBM PC compatible systems; DOS 3.1 amd higher Unix Version : 2.3 of 1993 Citation : Wallace J.C., Henikoff S. PATMAT: a searching and extraction program for sequence, pattern and block queries and databases. Comput. Appl. Biosci. 8:249-254(1992). Availability: Both MS-DOS and Unix versions are available by anonymous ftp from ncbi.nlm.nih.gov. The files to get (in binary mode) are: A) For DOS: In the "/repository/blocks/patmat.dos" directory. You should get all the files in that directory. B) For Unix: In the "/repository/blocks/patmat.unix" directory. You should get: README.patmat.unix patmat.tar.Z You should then, once the files are transferred: uncompress patmat.tar.Z tar -xvf patmat.tar Note: Executable files are included for SUN Sparc, DEC and Silicon Graphics workstations. Rename the appropriate file "patmat", e.g. mv sparcpatmat patmat Description : General database searching tool with a simple and clear user interface. Can searches PROSITE.DAT as a pattern database. Searches other databases with patterns as probes. ---------------------------------------------------------------------------- Programs : dbsite and mksite Authors : Jean-Michel Claverie, Isabelle Sauvaget, and Herve Recipon Address : National Center for Biotechnology Information NLM/NIH, Building 38A 8600 Rockville Pike Bethesda, MD 20894 USA Telephone: +1-301-4962475 Email : jmc@ncbi.nlm.nih.gov Runs on : Unix Language : C (code is available). Version : 2.0 of January 1992. Citation : Claverie J.-M., Sauvaget I. WOOB.C: a portable software package for defining and searching ambiguous sequence patterns Protein Seq. Data Anal. 4:119-121(1991). Availability: Send an email message to the first author. Description : dbsite searches a set of sequences (from one to an entire database) in FASTA format for patterns defined as position/ weight matrices. Pattern definition is straigthforward and scans are fast. Options include thresholding and both tabulated and re-entrant (e.g. FASTA format) outputs. mksite makes weight matrice patterns out of either multiple alignments or PROSITE patterns definition (PA line). ---------------------------------------------------------------------------- Program(s) : QUELSITE Author : C. Valencien Address : BISANCE - CITI2 45 rue des Saints-Peres 75270 Paris Cedex 06 France Telephone: +33-1-42962489 Email : bisance@frciti51.bitnet Runs on : VAX with VMS (Fortran) Version : June 1991. Citation : Dessen P., Fondrat C., Valencien C., Mugnier C. BISANCE: A French service for access to biomolecular sequence databases. Comput. Appl. Biosci. 6:355-356(1990). Description : QUELSITE is a program which is integrated in the BISANCE structure (national server in France). It permits to query all items of the PROSITE database as keywords, patterns, access or documentation numbers. ---------------------------------------------------------------------------- Program(s) : SIGNPT Author : Phillipe Dessen Address : Service de Bioinformatique CNRS - INSERM 7 rue Guy Moquet - BP8 94801 VILLEJUIF Cedex France Telephone: +33-1-45595241 Email : dessen@genome.vjf.inserm.fr Runs on : Unix or VMS Language : Fortran 77 Version : November 1992. Citation : Dessen P., Fondrat C., Valencien C., Mugnier C. BISANCE: A French service for access to biomolecular sequence databases. Comput. Appl. Biosci. 6:355-356(1990). Description : SIGNPT is a program which is integrated in the SQX package (EMBNet national server in France). It permits to search the PROSITE patterns on any protein sequence (personal or from PIR, SWISS-PROT databanks). Probability of occurence is evaluated from the mean abundance of amino acids in the database. A given level of mismatch is authorized. ---------------------------------------------------------------------------- Program : PATTERN Author : C. Geourjon and Gilbert Deleage Address : Institut de Biologie et Chimie des Proteines UPR 412-CNRS Universite Claude Bernard Lyon 1 7, passage du Vercors F-69367 Lyon Cedex 07 France Telephone: +33-72722647 Fax : +33-72722601 Email : deleage@ibcp.fr Runs on : IBM RISC 6000 under AIX (Unix), also available for DOS. Language : F77 Fortran. Version : 2.0 Citation : Geourjon C., Deleage G. Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins. Comput. Appl. Biosci. 9:87-91(1993). Availability: Can be obtained for non-commercial use; write to the authors or contact them by electronic mail. Description : Part of the ANTHEPROT software package for protein sequence analysis. Can scan a sequence with the patterns stored in the PROSITE.DAT file or with user-defind patterns stored using the same syntax. The user can set an optional similarity thresold or mismatch number. ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- 2) COMMERCIAL PROGRAMS ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Program(s) : PROSITE in the PC/Gene package Runs on : IBM PC compatible systems; DOS 3.1 and higher Version : 5.10 in PC/Gene release 6.8 Company info: IntelliGenetics, Inc. Address : IntelliGenetics 700 El Camino Real East Suite 300 Mountain View, CA 94040-2216 U.S.A. Telephone: +1-415-9627300 Fax : +1-415-9627302 Address : IntelliGenetics Belgium Amocolaan 2 B 2440 Geel Belgium Telephone: +32-3-2195352 Fax : +32-3-2195354 Description : This program is part of the PC/Gene protein and nucleotide sequence analysis package, it allows the user to scan a protein sequence for the occurence of PROSITE patterns. The output shows the list of hits in a tabular form as well as annotations under a standard three-letter code representation of the sequence. So as to expound the biological relevance of the sites detected in a sequence the program can display the documentation relevant to each pattern detected in a sequence. The PROSITE documentation file can also be searched for the occurence of one or more word(s). ---------------------------------------------------------------------------- Program(s) : QUEST in the IntelliGenetics Suite package Runs on : Sun with SunOS Version 4.0 or greater VAX with VMS 5.4 or greater Version : Release 5.4 of the IntelliGenetics Suite Company info: IntelliGenetics, Inc. Address : IntelliGenetics 700 El Camino Real East Suite 300 Mountain View, CA 94040-2216 U.S.A. Telephone: +1-415-9627300 Fax : +1-415-9627302 Address : IntelliGenetics Belgium Amocolaan 2 B 2440 Geel Belgium Telephone: +32-3-2195352 Fax : +32-3-2195354 Description : The QUEST program allows a user to scan a data bank for any pattern of characters in a sequence or annotations. Patterns can be entered by the user or can be taken from over 3000 known patterns provided with the program. These protein and nucleic acid patterns include those found in PROSITE, patterns in the Transcription Factors Database (TFD), and patterns entered from the literature by IntelliGenetics. You can also use QUEST to scan your sequence against the PROSITE data bank or any of the other patterns provided with the IntelliGenetics Suite. ---------------------------------------------------------------------------- Program(s) : PROSITE in the GeneWorks(R) Program Runs on : Apple MacIntosh; System 6.x and 7. Version : 4.0 in GeneWorks release 2.2.1 Company info: IntelliGenetics, Inc. Address : IntelliGenetics 700 El Camino Real East Suite 300 Mountain View, CA 94040-2216 U.S.A. Telephone: +1-415-9627300 Fax : +1-415-9627302 Address : IntelliGenetics Belgium Amocolaan 2 B 2440 Geel Belgium Telephone: +32-3-2195352 Fax : +32-3-2195354 Description : PROSITE is incorporated in three different parts of the GeneWorks program. All or a portion of the patterns described in PROSITE can be displayed in the sequence view of GeneWorks. The sites described in PROSITE can also be seen in GeneWorks' Graphic view, which shows a graphic schematic of the sequence and can compare the PROSITE graphic with other elements, such as plots of hydrophobicity, structure, and others. GeneWorks is also capable of searching all of the SWISS-PROT database for patterns. It is possible to enter any of the PROSITE patterns in GeneWorks Query view to search the data bank. The PROSITE documentation describing each of the patterns is available as on-line GeneWorks help. By selecting the pattern, the user can bring up a printable window containing the appropriate PROSITE help. ---------------------------------------------------------------------------- Program(s) : MOTIFS in the Wisconsin Package Runs on : VAX with VMS 5.0 or greater DEC-AXP with Open VMS 1.0 or greater Silicon Graphics (RISC) with IRIX Version 5.0 SUN (Sparc) with SunOS Version 4.1.3 or Solaris version 2.2 Version : 8.01 Company Info: Genetics Computer Group Address : 575 Science Drive Madison, WI 53711 U.S.A. Telephone: +1-608-2315200 Fax : +1-608-2315202 Email : help@gcg.com Description : MOTIFS looks for protein sequence motifs by checking your protein sequence for every sequence pattern in the PROSITE database. Symbol mismatches can be allowed. For each find, the output file displays the original complex pattern from the PROSITE database and the actual (simplified) pattern that was identified. As an option, the PROSITE documentation relevent to each 'found' pattern can be included in the output file. ---------------------------------------------------------------------------- Program(s) : PROMOT Runs on : Silicon Graphics IRIX, Hewlett Packard 700, SUN Sparcstations Is expected to be ported to VAX under VMS, Version : 1 Company Info: Oxford Molecular Ltd (OML) Address : Magdalen Centre Oxford Science Park Sandford-on-Thames Oxford OX4 4GA United Kingdom Telephone: +44-865-784600 Fax : +44-865-784601 Citation : Sternberg M.J.E. PROMOT: A FORTRAN program to scan protein sequences against a library of known motifs. Comput. Appl. Biosci. 7:257-260(1991). Description : PROMOT will scan one or more protein sequences against PROSITE. Statistics of the matches are evaluated. User-defined patterns can also be input. PROMOT will also scan one or more motifs against a protein sequence database in SWISS-PROT or PIR-NBRF formats. ---------------------------------------------------------------------------- Program(s) : Protean, GeneMan Runs on : Apple MacIntosh Company info: DNASTAR, Inc. Address : DNASTAR, Inc. 1228 South Park Street Madison, WI 53715 U.S.A. Telephone: +1-608-2587420 Fax : +1-608-2587439 Address : DNASTAR, Ltd. Abacus House, Manor Road West Ealing, London W13 OAS United Kingdom Telephone: +44-81-5668282 Fax : +44-81-5669555 Description : Protean and GeneMan are part of the LaserGene protein and DNA sequence analysis package. Protean allows the user to scan a protein sequence for the occurence of PROSITE patterns. GeneMan allows the user to scan a protein database for the occurence of PROSITE patterns. The output displays matches in a tabular form as well as graphically. The programs also display the documentation relevant to each pattern detected in a sequence. ---------------------------------------------------------------------------- Program(s) : SEQ/Pattern in PRO-EXPLORE 1.0 Runs on : All Silicon Graphics Operating system : IRIX 3.3 Graphics : gl_s run time library 24 bit planes for colour or RGB dithering 24 bit planes for Z-buffering ESV 3,3+,10,20,30,40,50 Operating system : ESos 2.0 Graphics : PEX 2.0 Company info: Biostructure SA Address : Les Algorithmes - Euclide - Parc d'Innovation F-67400 Illkirch-Graffenstaden France Telephone: +33-88679800 Fax : +33-88679801 Description : PRO-EXPLORE is a graphical protein modelling package. It provides tools for multi-sequence editing and alignment, sequence analysis, database investigation, and 3D modelling. With the menu SEQ/Pattern, you can manage pattern databases, and search for patterns in sequences. Pattern information can be extracted from PROSITE and used to create your own pattern database. The patterns of PROSITE or any other database can be used to scan a sequence. For each of the detected patterns, the database information is displayed , and the sequence is coloured accordingly. ---------------------------------------------------------------------------- Program(s) : Motif Master Runs on : IBM PC compatible systems; DOS 3.1 and higher Version : 1.0 Company info: National Biosciences Inc. Address : 3650 Annapolis Lane N., suite 140 Plymouth, MN 55447 U.S.A. Telephone: +1-612-5502012 or +1-800-7474362 Fax : +1-612-5509625 or +1-800-3695118 Email : nbi@biotechnet.com Author : Maltchenko S. Molecular Biology Department National Biosciences, Inc. Description : Motif Master searches protein sequence files or sequence databases against the PROSITE database. Files & databases may also be searched against user-generated databases or patterns. Search results (pattern matches) may be displayed on-screen or outputted to a file. Motif Master also searches the PROSITE documentation file, from which specific chapters may be retrieved. The program accepts DNA or RNA pattern databases as well, for searching nucleic acid sequence files. PIR, SWISS- PROT, EMBL and GenBank formats are all compatible with Motif Master as well as plain sequence files. ---------------------------------------------------------------------------- Program(s) : BIOSEARCH/PR Runs on : ? Version : ? Company info: Fujitsu Ltd. Address : 9-3 Nakase 1-Chome, Mihama-Ku Chiba-Shi Chiba 261 Japan Telephone: +81-43-? Fax : +81-43-299 3019 Email : ? Description : ? ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- 3) Electronic mail servers ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Name : EMBL Mail-PROSITE Server Organiz. : European Molecular Biology Laboratory (EMBL) / Heidelberg / Germany Description: Allows to rapidly compare a new protein sequence against all patterns stored in PROSITE. Address : prosite@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Note : Can also be used with WWW. ----------------------------------------------------------------------------- Name : BLOCKS e-mail searcher Organiz. : Fred Hutchinson Center / Seattle / USA Description: Compares a protein or DNA sequence to the current database of protein blocks. Blocks are short multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. The BLOCKS database has been constructed by successive application of the automated PROTOMAT system to individual entries in PROSITE. You can also use this server to retrieve specifics blocks and PROSITE entries. Address : blocks@howard.fhcrc.org Contact : To report problems: henikoff@howard.fhcrc.org ----------------------------------------------------------------------------- Name : MOTIF E-Mail Server on GenomeNet Organiz. : Supercomputer Laboratory / Institute for Chemical Research / Kyoto / Japan Description: Allows to rapidly compare a new protein sequence against all patterns stored in PROSITE as well as in the MotifDic library. Address : motif@genome.ad.jp Contact : To report problems: motif-manager@genome.ad.jp -End-of-document-------------------------------------------------------------