| EMBL FILE SERVER News Number 9, December 4th 1992 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Improvement of EMBL's Internet connectivity <3> Anonymous FTP services - alternative sites <4> New mail server command <5> Updates to data collections <6> Updates to software collection <7> Other updates <8> Summary of directories on the file server <9> Getting started ? <10> Network addresses at EMBL <1> Introduction ------------ The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail, anonymous FTP or Gopher. The service is free. <2> Improvement of EMBL's Internet connectivity ------------------------------------------- Recently there has been a improvement in EMBL's Internet connection which results in considerably faster access to our anonymous FTP server and to our Gopher server, and also a quicker response to e-mail file server requests. Please note that the FTP and Gopher servers both run on FTP.EMBL-Heidelberg.DE (192.54.41.33) Do not use the host name EMBL-Heidelberg.DE <3> Anonymous FTP services - alternative sites (a) The anonymous FTP archives at EMBL are mirrored by an FTP server managed by the Israeli EMBnet national node (INN) at the Weizmann Institute. Internet address: sunbcd.weizmann.ac.il (b) Complete copies of the EMBL quarterly releases are also available by anonymous FTP from: - Swiss EMBnet Node, Biozentrum der Universitaet Basel (Switzerland) Internet address: bioftp.unibas.ch [131.152.8.1] Maintained by Reinhard Doelz (doelz@comp.bioz.unibas.ch) Plain ASCII flat files. See the file DESCRIPTION in the top level directory for more information, also on other formats of data. - Department of Molecular Biology Massachusetts General Hospital Internet address: amber.mgh.harvard.edu [132.183.190.26] Maintained by Mike Cherry (CHERRY@Frodo.MGH.Harvard.EDU) Compressed EMBL flat files. See the 000readme.txt file in the EMBL directory for more information, also on other formats of data. <4> New mail server command ----------------------- The SIZE command was added to the set of commands recognised by the EMBL e-mail server. Because some mailer systems have a maximum file size limitation the EMBL mail server splits large files into parts. The default size of these packets is 95K but can be changed with the SIZE command. E.g. SIZE 30 would change the packet size to 30K, whereas SIZE 500 would set it to 500K. Note, however, that uuencoded files are stored in individual parts of 90K each on our server, so changing the packet size to larger values will have no effect on them. <5> Updates to Data Collections ------------------------------------ New databases have been added to the file server recently: (a) Steven Henikoff's BLOCKS database Henikoff, S. and Henikoff, J. G. (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19, 6565-6572. E-mail server: directory BLOCKS Anonymous ftp: /pub/databases/blocks (b) A database of CpG islands in the human genome (CPGISLE) Larsen, F., Gundersen, G., Lopez, L. and Prydz, H. (1992) CpG island as Gene Markers in the Human Genome. Genomics 13, 1095-1107. E-mail server: directory CPGISLE Anonymous ftp: /pub/databases/cpgisle (c) A database of protein kinase catalytic domains (PKCDD) provided by S.K. Hanks, A.M. Quinn and T. Hunter, Salk Institute. E-mail server: directory PKCDD Anonymous ftp: /pub/databases/pkcdd (d) Pre-release data from the Brookhaven Protein Data Bank (PDB) are now available in addition to the full releases. E-mail server: directory PROTEINDATA <6> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): The full path specifications for these files on the EMBL ftp server are shown in square brackets. DOS: ---- AUTHORIN.UAA (N) Sequence data submission tool (Intelligenetics/DDBJ/EMBL/GenBank) [/pub/software/dos/authorin.uaa to authorin.uaf] CODONS.UUE (N) Codon usage analysis (A. Lloyd and P. Sharp) [/pub/software/dos/codons.uue] CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/dos/cregex.c] DOTPLOT.UUE (N) Dot plot analysis (R> Nakisa) [/pub/software/dos/dotplot.uue] ESEE.UAA (U) Multiple sequence alignment editor v1.09e (E. Cabot) [/pub/software/dos/esee.uaa to esee.uac] FASTMAP.UAA (N) Approx. multipoint lod score calculation (D. Curtis) [/pub/software/dos/fastmap.uaa to fastmap.uac] GEPASI.UAA (N) Modelling of metabolic pathways (P. Mendes) [/pub/software/dos/gepasi.uaa to gepasi.uai] MACAW105.UAA (U) Multiple sequence editor v1.05 (G. Schuler) [/pub/software/dos/macaw105.uaa and macaw105.uab] PEDRAW14.UAA (U) Pedigree drawing program v1.4 (D. Curtis) [/pub/software/dos/pedraw14.uaa to pedraw14.uae] RAMHA.UAA (N) Monte Carlo simulation of random mutagenesis synthetic cDNA (D. Siderovski) [/pub/software/dos/ramha.uaa and ramha.uab] SAR2PCIT.UUE (N) Conversion of SeqAnalRef to ProCite format (E. Sonnhammer) [/pub/software/dos/sar2pcit.uue] SORFIND.UAA (N) Prediction of exons in vertebrate genomic DNA (G. Hutchinson) [/pub/software/dos/sorfind.uaa and sorfind.uab] TRBBS.UAA (N) File exchange program for automated fluorescent DNA sequencer data (I. Consani) [/pub/software/dos/trbbs.uaa and trbbs.uab] Mac: ---- AUTHORIN.HQX (N) Sequence data submission tool (Intelligenetics/DDBJ/EMBL/GenBank) [/pub/software/mac/authorin.hqx] DATAMINDER.HQX (N) Data management tools for molecular biologists (K. Usdin) [/pub/software/mac/dataminder.hqx] EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.1.1 (EMBL Data Library) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (N) Source code for EMBL-Search v2.1.1 [/pub/software/mac/embl-search_src.hqx] GBSEARCH-NCBI.HQX (U) Tool to assist access to GenBank servers at NCBI v2.0.2 (D. Gilbert) [/pub/software/mac/gbsearch-ncbi.hqx] GELREADER_FPU.HQX (N) NCSA's GelReader software for Macs with FPU [/pub/software/mac/gelreader_fpu.hqx] GELREADER_NO_FPU.HQX (N) NCSA's GelReader software for Macs w/o FPU [/pub/software/mac/gelreader_no_fpu.hqx] GELREADER_SAMPLES.HQX (N) Example files for NCSA's GelReader [/pub/software/mac/gelreader_samples.hqx] HYPERPCR.HQX (N) Calculation of PCR conditions (B. Osborne) [/pub/software/mac/hyperpcr.hqx] LOOPDLOOP.HQX (N) Tool for drawing RNA structures (D. Gilbert) [/pub/software/mac/loopdloop.hqx] MACPATTERN.HQX (U) Protein pattern searching with PROSITE and BLOCKS database v.2.0.1 (R. Fuchs) [/pub/software/mac/macpattern.hqx] MACT_GENERAL.HQX (N) MacT package for phylogenetic tree calculation (general programs and documentation) (Luettke) [/pub/software/mac/mact_general.hqx] MACT_TREE26.HQX (N) MacT package for phylogenetic tree calculation (TREE26 programs for up to 26 sequences) (Luettke) [/pub/software/mac/mact_tree26.hqx] MACT_TREE4.HQX (N) MacT package for phylogenetic tree calculation (TREE4 programs for four sequences) (Luettke) [/pub/software/mac/mact_tree4.hqx] MACT_TREE5.HQX (N) MacT package for phylogenetic tree calculation (TREE5 programs for five sequences) (Luettke) [/pub/software/mac/mact_tree5.hqx] PUPKIT.HQX (N) TrueType and Postscript fonts for displaying sequences in Puppy and Kitty representation (U. Melcher) [/pub/software/mac/pupkit.hqx] PUPPY.HQX (U) Special display of nucleic acid and protein sequences v2.0 (U. Melcher) [/pub/software/mac/puppy.hqx] STUFFITLITE.HQX (U) Compression/decompression/binhex program v3.0.3 (R. Lau) [/pub/software/mac/stuffitlite.hqx or stuffitlite.sea] YEASTSTRAINS.HQX (U) Strain management, in particular yeast (K. Froehlich) [/pub/software/mac/yeaststrains.hqx] UNIX: ----- CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/unix/cregex.c] ICATOOLS.UAA (N) Clustering and statistical analysis of large cDNA collections (J. Parsons) [/pub/software/unix/icatools.tar.Z] ICRF_CTG.UAA (N) Tools for ordering clone libraries based on hybridisation data (R. Mott and A. Grigoriev) [/pub/software/unix/icrf_ctg.tar.Z] ISSC.UAA (U) Sensitive sequence alignment package (Oct 92) (P. Argos et al.) [/pub/software/unix/issc.tar.Z] MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers v3.0 (T. deBoer) [/pub/software/unix/mailfasta.tar.Z] OVERSEER.UAA (U) Package for searching nucleic acid databases (Oct 92) (P. Sibbald) [/pub/software/unix/overseer.tar.Z] STATUS.UAA (N) Tools for managing large DNA-sequencing projects (M. Dubnik) [/pub/software/unix/status.tar.Z] ProtQuiz (N) Xwindows protein 3D/1D display (only available (M.Scharf, C.Sander) from FTP server) [/pub/software/unix/protquiz/ProtQuiz-0.9.tar.Z] VAX: ---- CDACCESS.UAA (U) Driver software for reading ISO CD-ROMs v2.05 (P. Stockwell) [/pub/software/vax/cdaccess.uaa and cdaccess.uab] CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/vax/cregex.c] GENEIDSHELLS.SHARE (N) DCL shells for using GENEID server (F. Macrides) [/pub/software/vax/geneidshells.share] GRAILSHELLS.SHARE (N) DCL shells for using GRAIL server (F. Macrides) [/pub/software/vax/grailshells.share] ICATOOLS.UAA (N) Clustering and statistical analysis of large cDNA collections (J. Parsons) [/pub/software/vax/icatools.uaa to icatools.uai] ISSC.UAA (U) Sensitive sequence alignment package (Oct 92) (P. Argos et al.) [/pub/software/unix/issc.uaa to issc.uak] NCBISHELLS.SHARE (N) DCL shells for using GenBank servers (F. Macrides) [/pub/software/vax/ncbishells.share] OVERSEER.UAA (U) Package for searching nucleic acid databases (Oct 92) (P. Sibbald) [/pub/software/unix/overseer.uue] SCRUTINE.UAA (U) Scrutineer, sequence database analysis, Nov 1992 (P. Sibbald) [/pub/softare/vax/scrutine.uaa to scrutine.uai] <7> Other updates ------------- (a) A new directory that will hold information for crystallographers, XRAY. The only file currently present is the list of e-mail addresses of crystallographers and related scientists maintained by M. Teeter, Boston College. E-mail server: directory XRAY Anonymous ftp: /pub/databases/xray (b) ALIGN directory: DS11144.DAT - Alignment of insect mtDNA and ND1 gene products. Submitted by D. Pashley, 12-Jun-1992 DS12100.DAT - Alignment of small subunit rRNAs from higher fungi. Submitted by J. Suguyama, 4-Sep-1992 <8> Summary of directories on the file server --------------------------------------- directories with updated information are marked by an asterisk. Anonymous ftp NetServ -------------- --------- * EMBL Nucleotide Sequence Database /pub/databases/embl NUC (Rel. 33, Dec 92 + updates) * Eukaryotic Promotor Database /pub/databases/epd EPD (Rel. 33, Nov 92) * SwissProt Protein Sequence Database /pub/databases/swissprot PROT (Rel. 23, Aug 92 + updates) * Prosite pattern database /pub/databases/prosite PROSITE (Rel. 9.10, Aug 92) * ENZYME database /pub/databases/enzyme ENZYME (Rel. 10.00, Aug 92) * Brookhaven Protein Databank not available PROTEINDATA (Rel. 61, Jul 92 + pre-release) * REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE (Rel. 9212, Dec 92) tRNA sequence and gene sequence db /pub/databases/trna TRNA (1991) * TFD, Transcription Factor Database /pub/databases/tfd TFD (Ver 5.5, Nov 92) * ECD, E.coli Database /pub/databases/ecd ECD (Rel. 13, Nov 92) * FLYBASE, Drosophila Genetic Map db /pub/databases/flybase FLYBASE (9209, 8-Sep-1992) * LiMB, Listing of Mol. Biol. db's /pub/databases/limb LIMB (Rel. 3.0) * SEQANALREF, Seq. analysis refs /pub/databases/reflist REFLIST (Rel. 32, Oct 92) FANS_REF, Functional analysis refs /pub/databases/reflist REFLIST (Rel. 3.4, Apr 91) Alu sequence database and alignment /pub/databases/alu ALU * Haemophilia B database /pub/databases/haemb HAEMB (Rel. 2, Dec 1992) Compilation of small RNA sequences /pub/databases/smallrna SMALLRNA (Oct 91) Berlin Databank of 5S rRNA and /pub/databases/berlin BERLIN 5S rRNA gene sequences (1991) Compilation of small ribosomal /pub/databases/rrna RRNA subunit RNA sequences (May 1992) CUTG, codon usage /pub/databases/cutg CUTG tabulated from GenBank rel. 69 3D_Ali, 3D alignment database /pub/databases/3d_ali 3D_ALI (March 1992) RLDB, Reference Library Database /pub/databases/rldb RLDB (April 1992) * CpG Islands Database /pub/databases/cpgisle CPGISLE (Pre-release 1.0, Oct 92) * Blocks database /pub/databases/blocks BLOCKS (Rel. 5.0, Jun 92) * HSSP, sequence-aligned protein /pub/databases/protein_extras/hssp families PROTEINDATA * FSSP, structure-aligned protein /pub/databases/protein_extras/fssp families (ftp only) * DSSP, protein secondary structures /pub/databases/protein_extras/dssp PROTEINDATA * pdb_select, representative sets of /pub/databases/protein_extras/ 3D proteins (ftp only) pdb_select Software: Software for MS-DOS computers /pub/software/dos DOS_SOFTWARE Software for Apple Macintosh /pub/software/mac MAC_SOFTWARE Software for UNIX /pub/software/unix UNIX_SOFTWARE Software for VAX/VMS /pub/software/vax VAX_SOFTWARE Other software /pub/software/misc MISC_SOFTWARE Miscellaneous: Technical documents, submission and /pub/doc DOC order forms, etc. Multiple DNA sequence alignments /pub/databases/embl/align ALIGN and consensus sequences Codon Usage tables /pub/databases/codonusage CODONUSAGE * Crystallographer's information /pub/databases/xray XRAY <9> Getting Started ? ----------------- For initial information, send standard electronic mail to the address: NetServ@EMBL-Heidelberg.DE containing just the word HELP on a line by itself. To use the anonymous ftp server, connect to the internet address FTP.EMBL-Heidelberg.DE using the username "anonymous" (without the quotes !) and giving your e-mail address as the password. Look in the directory /pub/help for various help files. To use the Gopher server, open a connection to FTP.EMBL-Heidelberg.DE at the standard Gopher port 70. <10> Network addresses at EMBL ------------------------- EMBL File Server (e-mail requests) NetServ@EMBL-Heidelberg.DE FASTA e-mail server FASTA@EMBL-Heidelberg.DE Quicksearch e-mail server Quick@EMBL-Heidelberg.DE Anonymous FTP FTP.EMBL-Heidelberg.DE Problems, feedback (human contact) NetHelp@EMBL-Heidelberg.DE EMBL Data Library enquiries DataLib@EMBL-Heidelberg.DE EMBL Data Library sequence submissions DataSubs@EMBL-Heidelberg.DE Software submissions and problems Software@EMBL-Heidelberg.DE