********************************** * EMBL FILE SERVER DOCUMENTATION * ********************************** EMBL Network File Server: NETSERV@EMBL.BITNET NETSERV@EMBL-HEIDELBERG.DE European Molecular Biology Laboratory Meyerhofstrasse 1 6900 Heidelberg West Germany Documentation version: April 1991. The EMBL Network File Server enables network access to the following: - The EMBL Nucleotide Sequence Database as well as the *newest* nucleotide sequence data created at EMBL and GenBank since the latest full release of the EMBL database - The SWISS-PROT Protein Sequence Database - The Brookhaven Protein Database (PDB) and other protein 3D structure data - Alu sequence database and alignment (ALU) - The Drosophila Genetic Map Database (DMAP) - The Escherichia coli Database (ECD) - The Enzyme Nomenclature Database (ENZYME) - The Eukaryotic Promoter Database (EPD) - The Listing of Molecular Biological Databases (LiMB) - The Dictionary of Protein Sites and Patterns (PROSITE) - The Restriction Enzyme Database (REBASE) - The Transcription Factor Database (TFD) - The Sequence analysis bibliography (SEQANALREF) - The Functional Analysis of Nucleotide Sequences bibliography (FANS_REF) - Free software for molecular biologists - Reference lists of relevance to molecular biology - General documents with importance to molecular biology - Documents describing the services of the EMBL Data Library Using the File Server --------------------- You use the file server by sending one or more of the above commands as electronic mail to the address NetServ@EMBL-Heidelberg.DE. The requested file(s) will then be returned to you by the file server. You must find out which operating system command you should use on your own computer (in order to be able to send electronic mail), and how to format the address NetServ@EMBL-Heidelberg.DE. The mail which you send to the file server should contain one file server command per line. Commands -------- The EMBL Network File Server supports the following commands: Help - sends a general help file Help - sends the help file on Get - sends the file Dir - sends a directory listing of Directories ----------- The files accessible via the file server are organised into directories. The following directories currently exist: NUC - Nucleotide Sequence data from the EMBL/GenBank databases PROT - SWISS-PROT Protein Sequence database PROTEINDATA - PDB protein 3D structure data ALU - Alu sequence database and alignment DROSOPHILA - Drosophila Genetic Map database ECD - Escherichia coli database ENZYME - Enzyme Nomenclature database EPD - Eukaryotic Promoter database LIMB - Listing of Molecular Biological databases PROSITE - Dictionary of Protein Sites and Patterns REBASE - Restriction Enzyme database REFLIST - Bibliography TFD - Transcription Factor Database DOS_SOFTWARE - Software for IBM PCs and clones (MS-DOS/PC-DOS) MAC_SOFTWARE - Software for the Apple MacIntosh UNIX_SOFTWARE - Software for UNIX VAX_SOFTWARE - Software for VAX/VMS SOFTWARE - General software and software information DOC - Documents with relevance to molecular biology ALIGN - Multiple DNA sequence alignments and consensus sequences CODONUSAGE - Codon Usage tables In general, the in the GET command begins with the name of the appropriate directory, followed by a colon. There should be no embedded blanks (spaces) between the directory name, the colon and the filename. Help ---- Help is available on the following topics: NUC PROT PROTEINDATA ALU DROSOPHILA ECD ENZYME EPD LIMB PROSITE REBASE REFLIST TFD SOFTWARE DOS_SOFTWARE MAC_SOFTWARE UNIX_SOFTWARE VAX_SOFTWARE DOC ALIGN CODONUSAGE Examples -------- Suppose you want to request: - general help on DOS software - a directory listing for the DOS software - the sequence called PIP03XX (nucleotide) - the sequence with accession number X03392 (nucleotide) - the sequence called KAP$YEAST (protein) - the new nucleotide sequence citation index (NEWCITATION.NDX) - the sequence submission form you could create a file containing the file server commands: HELP DOS_SOFTWARE DIR DOS_SOFTWARE GET NUC:PIP03XX GET NUC:X03392 GET PROT:KAP$YEAST GET NUC:NEWCITATION.NDX GET DOC:DATASUB.TXT and then mail that file to the address NetServ@EMBL-Heidelberg.DE Alternatively, you could type file server commands directly into the MAIL program. Please note that if the command you use to send mail allows you to specify a "subject", then anything you enter as the "subject" will be treated as a file server command. What will happen after you have sent your request(s) ---------------------------------------------------- You will receive back from the File Server message(s) containing the file(s) that you have requested. You should be aware of the following: 1) You will also receive a mail message that contains a log of what actions the File Server took when it received and processed your request(s). The subject line of this mail message looks like that: "Thanks for your call; here's the log ......" Example: Lets assume you have sent the following commands to the File Server: DIR EPD GET NUC:UNICORN.GENOME GET ENZYME:ENZYME.DAT The log message that you will receive back will look like that: dir epd * Directory sent. get nuc:unicorn.genmome * NUC:UNICORN.GENOME: file not found. get enzyme:enzyme.dat * ENZYME:ENZYME.DAT : file sent. * End of your requests. Thanks for your call ! 2) Some files are to big to be sent as a single mail message (the currrent size limit is 100 Kb). These files are automatically split into parts. Each of the mail messages that constitute such a file will have a subject line of the format: "Automatic response to : GET directory:filename (part n of m)" Please remember that the speed of mail file transfer normally depends on the file size. Therefore, you will probably receive smaller files much faster than larger files. This is of course also true for split files where the last part will travel faster than the rest. If you receive the last part, but *not* the others, you should check with your local computer centre whether there are any limitations on the size of files you are allowed to receive at your site. Unfortunately, there may be cases where you will not be able to receive files above a given size because mailers between EMBL and your site refuse to transfer them. News ----- Documentation of changes to the file server will be reported in the 'EMBL File Server News', available in the DOC directory of the file server: eg GET DOC:EMBL_Server_News.1 Feedback -------- If you have any problems using the file server, or suggestions as to how we might improve the service, please mail to the address NETHELP@EMBL- Heidelberg.DE. We want to hear from you! ============================================================================== ============================================================================== **************** * Help for NUC * **************** Contents: This directory contains all the sequence entries from the EMBL and GenBank nucleotide sequence databases as well as some documentation files (such as indices). -!- Important note -!- Entries from the latest full release of the EMBL Data Library are available, as well as data created at EMBL and Genbank since that release. It allow users to access a database entry as soon as it is created (at either EMBL or GenBank), instead of having to wait for up to three months for it to appear in the next release of the data bases on magnetic tape or on CD-ROM. The following files are available in the NUC directory: o Every entry in the current release of the EMBL Nucleotide Sequence database, and any new entry created after that release was built. Each entry is stored in a separate file; the filename is the same as the entryname. Entries can be accessed either by ENTRY NAME or by ACCESSION NUMBER. o Entries created by GenBank since their latest release are available and accessible by ACCESSION NUMBER. GenBank transmits daily their newly-generated data to EMBL electronically for this purpose. o The following indices built from entries new since the latest full releases of EMBL and GenBank databases. NEWSPECIES.NDX - Species index NEWAUTHOR.NDX - Author index NEWKEYWORD.NDX - Keyword index NEWSHORTDIR.NDX - Short directory index NEWCITATION.NDX - Citation index NEWACNUMBER.NDX - Accession number index o NEWENTRIES.NDX - A weekly listing of new EMBL and GenBank entries on the file server o USRMAN.DOC - The EMBL Nucleotide Sequence Database user manual which describes the format and conventions used in the database. o RELNOTES.DOC - Release Notes for the latest release of the EMBL Nucleotide Sequence Database o NARINFO.DOC - Documentation on the NAR data submission scheme. An example: A scientist reads about a sequence in a recent journal and wants to know if it exists yet as a database entry. They decide to obtain the citation index that includes only entries added to the database since the latest full release, by sending the following command to the file server: GET NUC:NEWCITATION.NDX They look up the reference, find that there is an entry called PIP03XX, and obtain a copy of it by sending the following command to the file server: GET NUC:PIP03XX If a database accession number is known, it can be used instead of the entry name, and of course there is then no need to get the citation index. ============================================================================== ============================================================================== ***************** * Help for PROT * ***************** Contents: This directory contains all the sequence entries from the SWISS- PROT Protein Sequence Database as well as some documentation files (such as indices). The following files are available in the PROT directory: o Every entry in the current release of the SWISS-PROT Protein Sequence Database. Each entry is stored in a separate file; the filename is the same as the entryname. Entries can be accessed either by ENTRY NAME or by ACCESSION NUMBER. o USRMAN.DOC - The SWISS-PROT Protein Sequence Database User's Manual which describes the format and conventions used in the database. o RELNOTES.DOC - Release notes for the latest release of the SWISS-PROT Protein Sequence Database An example: The following commands should be mailed to NETSERV@EMBL to get a copy of the SWISS-PROT entries B2MG$RAT and P01930 (accession number): GET PROT:B2MG$RAT GET PROT:P01930 ============================================================================== ============================================================================== ************************ * Help for PROTEINDATA * ************************ The following files are available in the ProteinData directory: o Protein Data Bank (Brookhaven) coordinate entries BRK.DIR - list of BRK entry names BRKNEW.DIR - list of new/changed entries in latest release BROOKDIR.DOC - header records for each BRK entry OBSLTE.DOC - list of obsolete entries protein.BRK - structure coordinates protein.BRK_MOD - model structure coordinates NEWSLETTER.DOC - latest PDB Newsletter examples: get PROTEINDATA:BROOKDIR.DOC get PROTEINDATA:2SEC.BRK o Coordinates of protein structures determined by x-ray crystallography at EMBL, in Brookhaven format. ROP2.BRK - rop wild type refined structure example: get PROTEINDATA:ROP2.BRK o Secondary structure digest of Protein Data Bank (Brookhaven) protein files, derived by a pattern recognition program DSSP (Definition of Protein Secondary Structure). The protein.DSSP files do not exist if the entry is for a protein, and at least the backbone coordinates are known. DSSP.DIR - list of DSSP filenames protein.DSSP - secondary structure for one protein example: get PROTEINDATA:1MBN.DSSP o Database of homology-derived protein structures alias: database of protein families alias: database of multiple sequence alignments One file for each PDB protein. Associated utility programs in source code for VMS or UNIX: HSSP.DIR - list of HSSP filenames protein.HSSP - secondary structure for one protein filter_hssp.for - filters a sequence family by your own criteria metric-gcg.data - exchange matrix required for filter_hssp find_hssp.com - finds a protein sequence in the database find_hssp.csh - table for use with find_hssp hssp_swissprot.table hssp_to_insight.for - prepares coloring by variability in 3D hssp_to_sybyl.for read_hssp.for - reads HSSP files example: get PROTEINDATA:1PPT.HSSP o Model coordinates from the 1986 and 1990 EMBO courses on protein design. TINY.BRK_MOD - tiny TIM BABA.BRK_MOD - babarellin BEAL.BRK_MOD - betaalphacin BUND.BRK_MOD - bundle FXNM.BRK_MOD - mutated flavodoxin FXNI.BRK_MOD - idealized flavodoxin RCU1.BRK_MOD - copper-binding rop GRENDEL.BRK_MOD - 4-helix membrane anchor FINGERCLASP.BRK_MOD - dimer of interdigitating beta-beta-alpha units SHPILKA.BRK_MOD - four-on-four antiparallel beta sandwich AIDA.BRK_MOD - designed anti-flavodoxin antibody LEATHER.BRK_MOD - minimal NAD binding domain example: get PROTEINDATA:TINY.BRK_MOD ============================================================================== ============================================================================== *********************** * Help for DROSOPHILA * *********************** Title : Drosophila genetic map database. Contents: Database of genetic and other information concerning the genetic loci of Drosophila melanogaster. Author : Michael Ashburner Dept. of Genetics University of Cambridge Cambridge England Electronic mail address: ma11@phx.cam.ac.uk Telephone: (+44 223) 333 969 The following files are available in the DROSOPHILA directory: o MAINDOC.TEXT - General documentation o FUNCTIONDOC.TEXT - Documentation of FUNCTION file o LOCIDOC.TEXT - Documentation of LOCI file o MAPDOC.TEXT - Documentation of MAPLOCI file o SYNONYMDOC.TEXT - Documentation of SYNONYMS file o FUNCTION.TEXT - Genes sorted by function o LOCI.TEXT - Genes sorted by gene symbols o MAPLOCI.TEXT - Genes sorted by map location o REFS.TEXT - References o SYNONYMS.TEXT - Table of synonyms PostScript files: The same files are also available as PostScript documents. They carry the extension .PS instead of .TEXT ============================================================================== ============================================================================== **************** * Help for ECD * **************** Title : Escherichia coli Database (ECD). Contents: ECD is a compilation of E. coli sequences which are present in the EMBL and GenBank databases and contains additional information on map locations of these sequences. Author : Manfred Kroeger and Ralf Wahl Institut fuer Mikro- und Molekularbiologie / Fachbereich Biologie Justus-Liebig-Universitaet Giessen Frankfurter Strasse 107 D-6300 Giessen Federal Republic of Germany Electronic mail address: kroeger@embl.bitnet The following files are available in the ECD directory: o ECD.DAT - ECD data file o ECD.DOC - Documentation for ECD For example, to get the documentation for the ECD database send a mail message to NETSERV@EMBL containing the command: GET ECD:ECD.DOC ============================================================================== ============================================================================== ******************* * Help for ENZYME * ******************* Title : Enzyme Nomenclature database (ENZYME). Contents: ENZYME contains the following data for each type of characterized enzyme for which an EC number has been provided: EC number, names (recommended and alternatives), catalytic activity, cofactor(s), pointers to SWISS-PROT enzyme sequence entries. Author : Amos Bairoch Dept. Medical Biochemistry C.M.U. 1, Rue Michel Servet 1211 Geneva 4 Switzerland Electronic mail address: bairoch@cgecmu51.bitnet Telephone: (+41 22) 61 84 92 The following files are available in the ENZYME directory: o ENZYME.DAT - ENZYME data file o ENZYME.USR - Documentation for ENZYME (User's Manual) For example, to get the User's Manual of ENZYME send a mail message to NETSERV@EMBL containing the command: GET ENZYME:ENZYME.USR ============================================================================== ============================================================================== **************** * Help for EPD * **************** Title : Eukaryotic Promoter Database (EPD). Contents: EPD provides information about eukaryotic promoters available in the EMBL nucleotide sequence Data Library and is intended to assist experimental researchers, as well as computer analysts, in the investigation of eukaryotic transcription signals. Author : Philipp Bucher Dept. of Mathematics Stanford University Stanford, CA 93405 USA Electronic mail address: bucher@gnomic.stanford.edu The following files are available in the EPD directory: o EPD.DAT - EPD data file o EPD.DOC - Documentation for EPD (User's Manual) For example, to get the documentation for the EPD database send a mail message to NETSERV@EMBL containing the command: GET EPD:EPD.DOC ============================================================================== ============================================================================== ***************** * Help for LiMB * ***************** Title : Listing of Molecular Biological Databases (LiMB). Contents: LiMB contains information about the contents of databases related to molecular biology as well as details of how they are maintained. Authors: Christian Burks / Principal Investigator Gifford Keen / Database Manager LiMB T-10, Mail Stop K710 Los Alamos National Laboratory Los Alamos, NM 87545 USA Electronic mail address: limb@lanl.gov Telephone: (+505) 667-9455 The following files are available in the LIMB directory: o LIMB.TXT - LiMB data file o LIMB.DOC - Documentation for LiMB o LIMBSHORT.TXT - Short form of LiMB o LIMB.NDX - Index file (keywords) For example, to get the documentation describing LiMB send a mail message to NETSERV@EMBL containing the command: GET LIMB:LIMB.DOC ============================================================================== ============================================================================== ******************** * Help for PROSITE * ******************** Title : Dictionary of protein sites and patterns (PROSITE). Contents: PROSITE is a compilation of sites and patterns found in protein sequences. Author : Amos Bairoch Dept. Medical Biochemistry C.M.U. 1, Rue Michel Servet 1211 Geneva 4 Switzerland Electronic mail address: bairoch@cgecmu51.bitnet Telephone: (+41 22) 61 84 92 The following files are available in the PROSITE directory: o PROSITE.DAT - PROSITE data file o PROSITE.DOC - Patterns documentation file o PROSITE.LIS - List of documentation chapters and patterns o PROSITE.USR - User's Manual o PROSITE_NEWS.n - PROSITE newsletters (where 'n' is a number) For example, to get the User's Manual of PROSITE send a mail message to NETSERV@EMBL containing the command: GET PROSITE:PROSITE.USR ============================================================================== ============================================================================== ******************* * Help for REBASE * ******************* Title : Restriction Enzyme Database (REBASE). Contents: REBASE is a listing of type 2 restriction enzymes. Author : Rich Roberts Cold Spring Harbor Laboratory Box 100 Cold Spring Harbor, NY 11724 USA Electronic mail address: roberts@cshl.org The following files are available in the REBASE directory: o REBASE.DAT - REBASE data file o REBASE.GCG - REBASE in a format compatible with the GCG package (for use with MAP) For example, to get the REBASE database send a mail message to NETSERV@EMBL containing the command: GET REBASE:REBASE.DAT ============================================================================== ============================================================================== ******************** * Help for REFLIST * ******************** Title : Contains: Sequence analysis references (SEQANALREF) and Functional Analysis of Nucleotide Sequences reference (FANS_REF) bibliography databases. 1) SEQANALREF Author : Amos Bairoch Dept. Medical Biochemistry C.M.U. 1, Rue Michel Servet 1211 Geneva 4 Switzerland Electronic mail address: bairoch@cgecmu51.bitnet Telephone: (+41 22) 61 84 92 2) FANS_REF Author : M.S.Gelfand Institute of Protein Research USSR Academy of Sciences, Pushchino Moscow Region, 142292 USSR Electronic mail address: cdp!gelfand@labrea.stanford.edu Note: in the SUBJECT field please write "For M.S.Gelfand" The following files are available in the REFLIST directory: o SEQANALREF.DAT - SEQANALREF data file o SEQANALREF.DOC - Documentation for SEQANALREF o FANS_REF.DAT - FANS_REF data file o FANS_REF.DOC - Documentation for FANS_REF For example, to get the SEQANALREF documentation file send a mail message to NETSERV@EMBL containing the command: GET REFLIST:SEQANALREF.DOC ============================================================================== ============================================================================== **************** * Help for DOC * **************** Contents: this directory is intended to contain files with general relevance to molecular biology like technical documents as well as submission and order forms. The following files are available in the DOC directory: o BIOSCI.DOC - Documentation for BIOSCI bulletin-board system. January 1991. o DATASUB.TXT - The Sequence Data Submission Form which can be used to submit a nucleotide and/or amino acid sequence. o DATASUB.DOC - Documentation on the sequence data submission scheme. o ORDERFORM.TXT - This form can be used to order the EMBL nucleotide database and the EMBL/SwissProt protein database on tape or CD-ROM. o ORDERINFO.TXT - This set of 6 short documents is subscription information distributed annually (May), and on demand, to people on the EMBL Data Library mailing list. o SUBMISSION.SW - The Software Submission Form can be used to submit molecular biology software for distribution on the EMBL File Server. o FT_DEFINITION.HQX - New common Feature Table Description (Macintosh, MS-WORD 4.0, StuffIt archive) o FT_DEFINITION.PS - New common Feature Table Description (PostScript version for Apple LW) o FT_DEFINITION.RTF - New common Feature Table Description (RTF version) o EMBNET.DOC - Description of the European Molecular Biology Data Network (EMBnet). ASCII version. October 1990 EMBNET.RTF - RTF version of EMBNET.DOC o EMBNET_JULY90.DOC - Report of EMBnet Workshop, Uppsala, July 1990 o SERVER.TXT - M. Gribskov's list of ftp sites and file servers with molecular biological data (Dec 1990) EMBL_Server_News - Reports of changes to the EMBL File Server. EMBL_Server_News.1 Number 1, October 12th 1990 EMBL_Server_News.2 Number 2, December 21st 1990 EMBL_Server_News.3 Number 3, February 12st 1991 GePSAN - Geneva Protein Sequence Analysis Newsletter by Amos Bairoch, University of Geneva, Switzerland GEPSAN.1 Volume 1, Number 1, January 1991 BIOBIT - An independent newsletter by Rob Harper, Helsinki, SF. Filenames Contents --------- ------------------------------------------------------- BIOBIT.1 Computer Viruses BIOBIT.2 BIONET BIOBIT.3 Introduction to TRICKLE BIOBIT.4 How to use RELAY BIOBIT.5 Introduction to FTP BIOBIT.6 Introduction to ARC and UUENCODE BIOBIT.7 Compression schemes BIOBIT.8 Current Contents on diskette BIOBIT.9 Introduction to EARN node names BIOBIT.10 Use of gateways from UK BIOBIT.11 EMBL Software File Server BIOBIT.12 Database function of LISTSERV BIOBIT.13 How to use the BIOSCI bulletin boards BIOBIT.14 ICGEB - International Center for Genetic Engineering and Biotechnology BIOBIT.15 GenBank Online Service BIOBIT.16 ANU News BIOBIT.17 BITNET User Guide BIOBIT.18 Using LISTSERV notebooks ============================================================================== ============================================================================== ********************* * Help for SOFTWARE * ********************* Molecular Biology Software on EMBL File Server ---------------------------------------------- Molecular biological software is available from the EMBL File Server for MS DOS computers, the Apple Macintosh, DEC VAX/VMS, and UNIX. Most of it will be distributed in a form that is first compressed and then converted from binary to a printable ASCII text file. The File Server delivers files by electronic mail, and thus cannot send executable files. To get further information use the File Server command: HELP DOS_SOFTWARE (details of how to access MS DOS software) DIR DOS_SOFTWARE (directory of MSDOS files available) HELP MAC_SOFTWARE (details of how to access Apple Macintosh software) DIR MAC_SOFTWARE (directory of Apple Macintosh files available) HELP UNIX_SOFTWARE (details of how to access UNIX software) DIR UNIX_SOFTWARE (directory of UNIX files available) HELP VAX_SOFTWARE (details of how to access VAX/VMS software) DIR VAX_SOFTWARE (directory of VAX/VMS files available) DIR SOFTWARE (directory of other available files) Submissions ----------- We would appreciate any submissions of software in this field. For further information fetch a copy of the software submission form: GET DOC:SUBMISSION.SW Distribution policy ------------------- The EMBL File Server is accessable without any restrictions to anyone with a network connection to the EMBL computer. Therefore it is up to the submitting author to include any copyright statements, shareware demands and limitations of usage and redistribution in the accompanying documentation file. To monitor distribution EMBL will keep a log of requests for each program. This information will be made available on the File Server to everyone. Problems -------- Please direct questions, bug reports, submissions, etc., to: EMBL Data Library Meyerhofstr. 1 D-6900 Heidelberg, FRG tel.: +49-6221-387258 E-mail: SOFTWARE@EMBL-Heidelberg.DE ============================================================================== ============================================================================== ************************* * Help for DOS_SOFTWARE * ************************* MS DOS Molecular Biology Software on EMBL File Server ----------------------------------------------------- Molecular biological software for IBM PC and clones is available from the EMBL File Server. Though all programs are tested we can make no warranty on the functionality of these programs nor shall be liable for any damage resulting from their usage. Most programs on the File Server are freeware, but that does not imply that there are no rights reserved by the authors. Some programs are shareware. You may freely copy and distribute these programs, but if you like to use them after a trial period you are asked to send the author a small fee. Please see the accompanying documentation files or manuals for details of copyright status. To get any file from the EMBL File Server use normal E-mail addressed to NETSERV@EMBL.BITNET. The body of the mail message should contain one server command per line. Getting started --------------- MS DOS software on the EMBL File Server is distributed in a form that is first compressed and then converted from binary to printable ASCII code ("uuencoded"). The standard extension for uuencoded files is ".uue". We recommend the use of Dumas' UUD program for decoding ".uue" files. How to get this program? a) You have access to a C compiler: Then download the source code for UUD by sending the command line: GET DOS_SOFTWARE:UUD.C Transfer it to your PC (e. g. using Kermit) and compile it. b) You have access to a Pascal compiler or to GWBASIC: Get the source code for a bootstrap uudecoder using GET DOS_SOFTWARE:UUD19.BAS or GET DOS_SOFTWARE:UUDECODE.PAS (resp.) Transfer it to your PC and compile it. These decoders can now in turn be used to get a copy of the recommended decoder UUD.EXE from the EMBL File Server. First request the file UUEMBL.UUE: GET DOS_SOFTWARE:UUEMBL.UUE Again, transfer this file to your PC and use either UUD19.EXE or UUDECODE.EXE to decode it: > UUD19 UUEMBL.UUE or > UUDECODE UUEMBL.UUE (resp.) You will get a file called UUEMBL.EXE. Run it, and it will extract itself to yield the UUD.EXE decoder and additionally the program UUE.EXE that is used to create the .UUE files at the EMBL. Use UUD.EXE for all further ASCII-binary conversions. We tested UUD.C with Turbo C and UUDECODE.PAS with Turbo Pascal. If you have problems compiling these sources with other compilers, please contact us. Note for users in the UK: While passing through the JANET/EARN gateway mail messages are often corrupted by character conversions. The caret character is replaced by a tilde. These conversions are not detected by UUD19. UUD19 will decode UUEMBL.UUE without an error message, but the resulting UUEMBL.EXE program will cause a system crash. Therefore check the UUEMBL.UUE file for occurrences of the tilde character and replace them by caret characters before decoding it. How to access files ------------------- All software for MS DOS on the EMBL File Server is in server directory called DOS_SOFTWARE, and a directory listing can be acquired with the file server command: DIR DOS_SOFTWARE To get any specific file use the command: GET DOS_SOFTWARE:filename.ext Transfer this file to your PC (e. g. using kermit). For decoding a uuencoded file run UUD and specify the source file name: > UUD filename.UUE Very large files are split into parts. The first part is designated "filename.UAA", the second part "filename.UAB" and so forth. UUD will automatically join the related files in correct order. The code generated from UUDECODE.PAS or UUD19.BAS does *NOT* support file splitting. To decode split files make sure that all belonging parts are in one directory and type: > UUD filename.UAA The name of the resulting file is stored within the ".uue" file; it will be placed in your current directory. The outcome of this procedure is a so-called "self-extracting archive" with a filename "filename.EXE". Just run it and it will create the final program and documentation files: > filename Attention: the filename of the archive may in some cases be different from the filename of the UUE or UAA files and may contain an additional "$" dollar character. Check that by doing a DIR *.EXE after the uudecoding. Record of requests ------------------ To facilitate communication between users of provided software and to give software authors some information on who has obtained copies of their programs, the File Server keeps a log of requests for each program by storing the sender's E-mail address in a file named "filename.LOG". For example, to get the log for the MSDOS program OLIGO use the command: GET DOS_SOFTWARE:OLIGO.LOG Problems -------- If you have any problems or questions contact: EMBL Data Library Meyerhofstr. 1 D-6900 Heidelberg, FRG tel.: +49-6221-387258 E-mail: SOFTWARE@EMBL-Heidelberg.DE ============================================================================== ============================================================================== ************************* * Help for MAC_SOFTWARE * ************************* Apple Macintosh Molecular Biology Software on EMBL File Server -------------------------------------------------------------- Molecular biological software for the Apple Macintosh is available from the EMBL File Server. Though all programs are tested we can make no warranty on the functionality of these programs nor shall be liable for any damage resulting from their usage. Most programs on the File Server are freeware, but that does not imply that there are no rights reserved by the authors. Some programs are shareware. You may freely copy and distribute these programs, but if you like to use them after a trial period you are asked to send the author a small fee. Please see the accompanying documentation files or manuals for details of copyright status. To get any file from the EMBL File Server use normal E-mail addressed to NETSERV@EMBL.BITNET. The body of the mail message should contain one server command per line. Getting started --------------- The Macintosh software on the EMBL File Server is distributed in a form that is first compressed and then converted from binary to printable ASCII. The program that is used to compress and encode Macintosh files is called StuffIt v1.5. The standard extension for stuffed files is ".hqx". You will first need to obtain a copy of the "unstuffing" utilities StuffIt (shareware) or the combination BinHex4/UnStuffIt (freeware). Since no source code is available please ask your Macintosh user group or your local Mac guru. How to access files ------------------- All software for the Macintosh on the EMBL File Server is in a directory called MAC_SOFTWARE, and a directory listing can be acquired with the file server command: DIR MAC_SOFTWARE To get any specific file use the command: GET MAC_SOFTWARE:filename.ext Transfer this file to your Macintosh (e. g. using Kermit with file type set to ASCII). For decoding a stuffed file run StuffIt and use the option "Decode BinHex-File" or use BinHex4. The resulting archive "filename.sit" stores the program files in compressed form. Open the archive from within (Un)StuffIt and extract them. For details of unstuffing and extraction please consult the StuffIt documentation. Very large files are split into parts. Use any word processor to remove the header lines and join the parts. Make sure to save the resulting file in text-only mode. Then use BinHex or (Un)StuffIt for conversion. Record of requests ------------------ To facilitate communication between users of provided software and to give software authors some information on who has obtained copies of their programs, the File Server keeps a log of requests for each program by storing the sender's E-mail address in a file named "filename.LOG". For example, to get the log for the Mac program MATMETH use the command: GET MAC_SOFTWARE:MATMETH.LOG Problems -------- If you have any problems or questions contact: EMBL Data Library Meyerhofstr. 1 D-6900 Heidelberg, FRG tel.: +49-6221-387258 E-mail: SOFTWARE@EMBL-Heidelberg.DE ============================================================================== ============================================================================== ************************** * Help for UNIX_SOFTWARE * ************************** UNIX Molecular Biology Software on EMBL File Server -------------------------------------------------- Molecular biological software for the UNIX operating system is available from the EMBL File Server. Though all programs are tested we can make no warranty on the functionality of these programs nor shall be liable for any damage resulting from their usage. Most programs on the File Server are freeware, but that does not imply that there are no rights reserved by the authors. Some programs are shareware. You may freely copy and distribute these programs, but if you like to use them after a trial period you are asked to send the author a small fee. Please see the accompanying documentation files or manuals for details of copyright status. To get any file from the EMBL File Server use normal E-mail addressed to NETSERV@EMBL.BITNET. The body of the mail message should contain one server command per line. Getting started --------------- UNIX software on the EMBL File Server is distributed in a form that is first compressed and then converted from binary to printable ASCII ("uuencoded"). The standard extension for uuencoded files is ".uue". You will first need to install the decoding program UUD on your machine. Get the C source code from the EMBL File Server using the command: GET UNIX_SOFTWARE:UUD.C and compile it: % cc -o uud uud.c The programs that are used for data compression are the standard UNIX tar and compress programs. How to access files ------------------- All software for UNIX on the EMBL File Server is in a directory called UNIX_SOFTWARE, and a directory listing can be acquired with the file server command: DIR UNIX_SOFTWARE To get any specific file use the command: GET UNIX_SOFTWARE:filename.ext For decoding a uuencoded file run uud and specify the source file name: % uud filename.uue Very large files are split into parts. The first part is designated "filename.uaa", the second part "filename.uab" and so forth. uud will automatically join the related files in correct order. To decode split files make sure that all belonging parts are in one directory and type: % uud filename.uaa The name of the resulting file is stored within the ".uue" file; it will be placed in your current directory. In most cases, the file name will end with .tar.Z Now use the UNIX uncompress program to expand these files: % uncompress filename.tar.Z which will result in a file named filename.tar in your current directory. Finally, use tar to extract all files from these archives: % tar -xvf filename.tar This will extract all files contained in the archive into your default directory. Record of requests ------------------ To facilitate communication between users of provided software and to give software authors some information on who has obtained copies of their programs, the File Server keeps a log of requests for each program by storing the sender's E-mail address in a file named "filename.LOG". For example, to get the log for the UNIX program SIGSEQ use the command: GET UNIX_SOFTWARE:SIGSEQ.LOG Problems -------- If you have any problems or questions contact: EMBL Data Library Meyerhofstr. 1 D-6900 Heidelberg, FRG tel.: +49-6221-387258 E-mail: SOFTWARE@EMBL-Heidelberg.DE ============================================================================== ============================================================================== ************************* * Help for VAX_SOFTWARE * ************************* VAX Molecular Biology Software on EMBL File Server -------------------------------------------------- Molecular biological software for the DEC VAX running VMS is available from the EMBL File Server. Though all programs are tested we can make no warranty on the functionality of these programs nor shall be liable for any damage resulting from their usage. Most programs on the File Server are freeware, but that does not imply that there are no rights reserved by the authors. Some programs are shareware. You may freely copy and distribute these programs, but if you like to use them after a trial period you are asked to send the author a small fee. Please see the accompanying documentation files or manuals for details of copyright status. To get any file from the EMBL File Server use normal E-mail addressed to NETSERV@EMBL.BITNET. The body of the mail message should contain one server command per line. Getting started --------------- VAX software on the EMBL File Server is distributed in a form that is first compressed and then converted from binary to printable ASCII ("uuencoded"). The standard extension for uuencoded files is ".uue". You will first need to install the decoding program UUD on your machine. Get the C source code from the EMBL File Server using the command: GET VAX_SOFTWARE:UUD.C and compile it. The program that is applied for compressing VMS files is called "ZOO". It is available in uuencoded form from the file server. GET VAX_SOFTWARE:ZOO.UUE Follow the procedure given below to decode it to ZOO.EXE. To be able to run these program insert the following lines in your login.com procedure: $ UUD :== $ your_directory:UUD $ ZOO :== $ your_directory:ZOO (your_directory must be replaced by the name of the directory where these programs are actually located). How to access files ------------------- All software for VAX VMS on the EMBL File Server is in a directory called VAX_SOFTWARE, and a directory listing can be acquired with the file server command: DIR VAX_SOFTWARE To get any specific file use the command: GET VAX_SOFTWARE:filename.ext For decoding a uuencoded file run UUD and specify the source file name: $ UUD filename.UUE Very large files are split into parts. The first part is designated "filename.UAA", the second part "filename.UAB" and so forth. UUD will automatically join the related files in correct order. To decode split files make sure that all belonging parts are in one directory and type: $ UUD filename.UAA The name of the resulting file is stored within the ".uue" file; it will be placed in your current directory. It will in most cases have the extension ".ZOO". These ZOO-archives have to be extracted by ZOO to obtain the executable programs and documentation. Use the command: $ ZOO E filename This will extract all files contained in the archive into your default directory. Record of requests ------------------ To facilitate communication between users of provided software and to give software authors some information on who has obtained copies of their programs, the File Server keeps a log of requests for each program by storing the sender's E-mail address in a file named "filename.LOG". For example, to get the log for the VAX/VMS program CLUSTAL use the command: GET VAX_SOFTWARE:CLUSTAL.LOG Problems -------- If you have any problems or questions contact: EMBL Data Library Meyerhofstr. 1 D-6900 Heidelberg, FRG tel.: +49-6221-387258 E-mail: SOFTWARE@EMBL-Heidelberg.DE ==============================================================================