From NETSERV@EMBL-Heidelberg.DE Fri Mar 6 20:34:07 1992 Received: from sirius.EMBL-Heidelberg.DE by convex.csc.fi with SMTP id AA20425 (5.65c8+/IDA-1.4.4 for ); Fri, 6 Mar 1992 10:11:46 +0200 Date: Fri, 6 Mar 1992 09:13 +0100 From: NETSERV@EMBL-Heidelberg.DE Subject: Reply to: HELP To: Martti.Tolvanen@convex.csc.fi Errors-To: PostMaster@EMBL-Heidelberg.DE Message-Id: X-Organization: European Molecular Biology Laboratory, Heidelberg. X-Envelope-To: Martti.Tolvanen@convex.csc.fi X-Vms-To: in%"Martti.Tolvanen@convex.csc.fi" Status: OR HELP [GENERAL] DIR [GENERAL] The EMBL Network File Server enables network access to the following: - EMBL Nucleotide Sequence Database. - The *newest* nucleotide sequence data created at EMBL *and* GenBank since the latest full release of the EMBL database. - DNA sequence alignments and consensus sequences - Swiss-Prot Protein Sequence Database - Brookhaven Protein Database and other structure (alignment) data (DSSP, HSSP) - Prosite Pattern Database - Transcription Factor Database (TFD) - Eukaryotic Promotor Database (EPD) - E. coli Database (ECD) - LiMB (Listing of molecular biological databases) Database - Restriction Enzyme Database (REBASE) - ENZYME Database - Drosophila Genetic Map Database (FlyBase) - Alu sequence database - Haemophilia B database (HAEMB) - Compilation of small RNA sequences (SMALLRNA) - tRNA sequence and tRNA gene sequence database - Berlin Databank of 5S rRNA and 5S rRNA gene sequences - Compilation of small ribosomal subunit RNA sequences - Codon usage tables - Compilation of codon frequencies tabulated from the GenBank nucleotide sequence database (CUTG) - 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 commands shown below 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 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 Network File Server at the European Molecular Biology Laboratory supports the following commands: Help - sends a general help file (this file) Help - sends the help file and directory listing of Get - sends the file Dir - same as Help Directories ----------- The files accessible via the file server are organised into directories. The following directories exist: Nuc - Nucleotide Sequence data from the EMBL and GenBank sequence databases. Prot - The SWISS-Prot Protein Sequence Database ProteinData - Protein structure data ProSite - ProSite Pattern Database ECD - E. coli Database ENZYME - The ENZYME database TFD - Transcription Factor Database EPD - Eukaryotic Promotor Database LiMB - Listing of Molecular Biological Databases REBASE - Restriction Enzyme database Flybase - Drosophila genetic map database HaemB - Haemophilia B database SmallRNA - Compilation of small RNA sequences tRNA - tRNA database Berlin - Berlin Databank of 5S rRNA and 5S rRNA gene sequences rRNA - Compilation of small ribosomal subunit RNA sequences Alu - Alu sequence database CodonUsage - Codon usage tables Align - DNA sequence alignments and consensus sequences RefList - Bibliographies, Reference lists DOS_Software - Free software for IBM PCs and clones Mac_Software - Free software for the Apple Macintosh VAX_Software - Free software for VAX/VMS UNIX_Software - Free software for UNIX Software - General software and software information Doc - Documents with relevance to molecular biology (Submission forms, technical documents etc.) CUTG - Compilation of codon frequencies tabulated from the GenBank nucleotide sequence database 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 ---- Further help is available on the following topics: Nuc Prot ProteinData ProSite ECD ENZYME EPD LIMB Doc REBASE RefList Software DOS_Software Mac_Software VAX_Software UNIX_Software Flybase Align CodonUsage TFD Alu tRNA HaemB SmallRna Berlin rRNA CUTG Examples -------- To request: - specific help on the sequence databases - general help on software - the sequence called PIP03XX (nucleotide) - the sequence with accession number X03392 (nucleotide) - the sequence called WAP$MOUSE (protein) - the new nucleotide sequence citation index (NEWCITATION.NDX) - the sequence submission form you could create a file containing the file server commands: HELP NUC HELP PROT HELP SOFTWARE GET NUC:PIP03XX GET NUC:X03392 GET PROT:WAP$MOUSE 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 your 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. File splitting -------------- Some files available from NETSERV are much larger than 100k. Although this should be no problem for today's computer network technology, there are still some mailer systems which refuse to transport "large" files. To accommodate most of our users we automatically split files in packets of approx. 95k. The Subject lines of the messages received from NETSERV give you information about how many packets were sent and about the part number of each packet. This should allow you to reconstruct the original file by joining the individual parts. 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! Summary of directories available on the EMBL File Server: -------------------------------------------------------- Databases: EMBL Nucleotide Sequence Database NUC (Rel. 29, Dec 91 + newest data from EMBL/GenBank/DDBJ) Eukaryotic Promotor Database (Rel. 29, Nov 91) EPD SwissProt Protein Sequence Database PROT (Rel. 20, Nov 91 + newest data) Prosite pattern database (Rel. 8.0, Dec 91) PROSITE ENZYME database (Rel. 7.00, Nov 91) ENZYME Brookhaven Protein Structure Database (Rel. 58, Oct 91) PROTEINDATA REBASE, Restriction Enzyme Database (Rel. 9201, Jan 92) REBASE tRNA sequence and gene sequence database (1991) TRNA TFD, Transcription Factor Database (Ver 4.0, Dec 91) TFD The E.coli Database (Rel. 9, Nov 91) ECD Drosophila Genetic Map Database (9201, 6-Jan-1992) FLYBASE Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB Sequence analysis bibliography (SEQANALREF Rel. 22, Dec 91) REFLIST Functional Analysis of Nucleotide Sequences bibliography REFLIST (FANS_REF Rel. 3.4, Apr 91) Alu sequence database and alignment ALU Haemophilia B database (Dec 1991) HAEMB Compilation of small RNA sequences (Oct 91) SMALLRNA Berlin Databank of 5S rRNA and 5S rRNA gene sequences (1991) BERLIN Compilation of small ribosomal subunit RNA sequences (1991) RRNA Compilation of codon frequencies tabulated from the CUTG GenBank database (based on GB rel. 69) Software: Software for MS-DOS computers DOS_SOFTWARE Software for Apple Macintosh MAC_SOFTWARE Software for UNIX UNIX_SOFTWARE Software for VAX/VMS VAX_SOFTWARE Other software, GenBank Clearinghouse, etc. MISC_SOFTWARE Miscellaneous: Technical documents, submission and order forms, etc. DOC Multiple DNA sequence alignments and consensus sequences ALIGN Codon Usage tables CODONUSAGE 27-Feb-1992