From usenet.ucs.indiana.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!gatech!swrinde!cs.utexas.edu!uunet!biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!fuchs Wed Jul 7 10:50:21 EST 1993 Article: 110 of bionet.molbio.embldatabank Path: usenet.ucs.indiana.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!gatech!swrinde!cs.utexas.edu!uunet!biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!fuchs From: fuchs@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server Newsletter 10 Message-ID: <1993Jul7.150539.100470@embl-heidelberg.de> Date: 7 Jul 93 14:05:39 GMT Reply-To: NetHelp@EMBL-Heidelberg.DE Organization: EMBL, European Molecular Biology Laboratory Lines: 480 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 10, July 7th 1993 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 69012 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Blitz e-mail server <3> Updates to data collections <4> Updates to software collection <5> Other updates <6> Summary of directories on the file server <7> Getting started ? <8> 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> Blitz e-mail server ------------------- BLITZ is an automatic electronic mail server for the MPsrch program of Shane Sturrock and John Collins, Biocomputing Research Unit, University of Edinburgh, Scotland. MPsrch allows you to perform sensitive and extremely fast comparisons of your protein sequences against the Swiss-Prot protein sequence database using the Smith and Waterman best local similarity algorithm. It runs on the MasPar family of massively parallel machines; the BLITZ server uses a 4096-processor MasPar MP-1 system. A typical search time for a query sequence of 400 amino acids is approximately 40 seconds to search the entire Swiss-Prot database. Additional time is required to reconstruct the alignments; the time for this will depend on the number of alignments requested. MPsrch is the fastest implementation of the SW algorithm currently available on any machine. How to use BLITZ ---------------- Send a properly formatted electronic mail message to BLITZ@EMBL-Heidelberg.DE containing required commands and parameters and the answer will be automatically mailed to you. To obtain full documentation of the service and algorithms used, send a message containing just the word HELP. If you have any problems using the BLITZ service, or any questions, please send them to: NETHELP@EMBL-Heidelberg.DE Example ------- SEQ STKKKPLTQE QLEDARRLKA IYEKKKNELG LSQESVADKM GMGQSGVGAL FNGINALNAY NAALLAKILK VSVEEFSPSI AREIYEMYEA VSMQPSLRSE YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEFT FKKLIRDSGQ VFLQPLNPQY PMIPCNESCS VVGKVIASQW PEETFG END The possible parameters (eg gap penalty, weight matrix) are explained in the HELP documentation. <3> Updates to Data Collections ------------------------------------ New databases have been added to the file server since Newsletter issue 9: (a) RELIBRARY - Restriction Enzyme List, by E. Raschke Raschke, E. (1993) Comprehensive restriction enzyme lists to update any DNA sequence computer program. Genetic Analysis, Techniques and Applications, Vol. 10, in press. (b) REPBASE - Protoypic sequences for human repetitive DNA, by J. Jurka Jurka, J., Walichiewicz, J. and Milosavljevic, A. (1992) J. Mol. Evol. 35:286 (c) HLA - Alignments of human class I and II HLA sequences, by S. Marsh, J. Zemmour and P. Parham. (d) TRANSTERM - Translational termination signal database, by C. Brown Brown, C.M., Dalphin, M.E., Stockwell, P.A., Tate, W.P. (1993) Nucleic Acids Res. Supplement, submitted (e) LISTA - Compilation of nucleotide sequences encoding proteins from the yeast saccharomyces, by P. Linder Mosse, M.O., Linder, P., Lazowska, J. and Slonimski, P.P. (1993) Curr. Genet. 23, 66. <4> 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: ---- BED.UAA (N) Sequence editor with speaker feeback (R. Hwan-Seok) [/pub/software/dos/bed.uaa and .uab] BOXSHADE.UUE (N) Plots of multiple alignments with boxes and shades (K. Hofmann) [/pub/software/dos/boxshade.uue] CM.UAA (U) Restriction map construction from multiple digestion data v1.0a (K. Hofmann) [/pub/software/dos/cm.uaa to cm.uai] CONSENSE.UUE (N) Calculation of consensus sequence from alignment (S. Rensing) [/pub/software/dos/consense.uue] DIGEST.UAA (N) Restriction enzyme mapping (R. Nakisa) [/pub/software/dos/digest.uaa and digest.uab] DOTPLOT.UAA (U) Dot plot analysis v3.0 (R. Nakisa) [/pub/software/dos/dotplot.uaa and dotplot.uaa] EXPLORE.UAA (N) Analysis of multiple alignments (G. Golding) [/pub/software/dos/explore.uaa and explore.uab] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/dos/hth.c] RASMOL.UAA (N) Visualisation of macromolecules using PDB files (R. Sayle) [/pub/software/dos/rasmol.uaa to rasmol.uac] SILMUT.UUE (N) Identification of regions suitable for silent mutagenesis (B. Shankarappa) [/pub/software/dos/silmut.uue] SORFIND.UUE (U) Prediction of exons in vertebrate genomic DNA v1.7 (G. Hutchinson) [/pub/software/dos/sorfind.uue] WINBLAST.UAA (N) Windows 3.1 interface for NCBI BLAST server (A. Sivaprasad) [/pub/software/dos/winblast.uaa to winblast.uae] WINDOT.UAA (N) Dot plot analyis under Windows 3.1 (R. Nakisa) [/pub/software/dos/windot.uaa and windot.uab] WINIRX.UAA (N) Windows 3.1 interface for NCBI IRX server [/pub/software/dos/winirx.uaa to winirx.uae] WINSEQ.UUE (N) Windows version of D. Gilbert's READSEQ (R. Nakisa) [/pub/software/dos/winseq.uue] Mac: ---- ALIGN.HQX (U) Sequence alignments and phylogeny (replacement of corrupt archive) (D. Feng) [/pub/software/mac/align.hqx] AMPLIFY.HQX (U) PCR primer checks v1.2 (B. Engels) [/pub/software/mac/amplify.hqx] BKGCUCLC_FONTS.HQX (N) Color fonts for use with sequence editors (M. Sogin) [/pub/software/mac/bkgcuclc_fonts.hqx] DBCONV.HQX (U) Transformation of line-oriented databases into tab- delimited format v2.0 (J. Valverde) [/pub/software/mac/dbconb.hqx] DIGISPEAK.HQX (N) Sequence reading with sonic digitizer (N. Mantei) [/pub/software/mac/digispeak.hqx] DNAID.HQX (U) DNA sequence editor with grep-like search routine v1.8 (F. Dardel) [/pub/software/mac/dnaid.hqx] EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.3.2 (EMBL Data Library) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (U) Source code for EMBL-Search v2.3.2 [/pub/software/mac/embl-search_src.hqx] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/mac/hth.c] LABHELPER.HQX (N) General laboratory tools for buffer preps etc. (T. Tzeng) [/pub/software/mac/labhelper.hqx] MACCLADE30_DEMO.HQX (N) Demo of phylogenetic analysis program (W. Maddison) [/pub/software/mac/macclade30_demo.hqx] MACP12.HQX (N) Protein property profile plots (A. Luettke) [/pub/software/mac/macp12.hqx] MACPATTERN.HQX (U) Protein pattern searching with PROSITE and BLOCKS database v3.0 (R. Fuchs) [/pub/software/mac/macpattern.hqx] MACSTAN.HQX (N) Random nucleotide sequence generator and analyzer (F. Gast) [/pub/software/mac/macstan.hqx] PROTEINSTRUCTURE.HQX (N) Tutorial on protein structures (C. Burchill) [/pub/software/mac/proteinstructure.hqx] READSEQ.HQX (U) Sequence format conversion program (D. Gilbert) [/pub/software/mac/readseq.hqx] RRNA-STACK.HQX (U) Phylogeny of 16/18S rRNA (J. Brown) [/pub/software/mac/rrna-stack.hqx] STUFFITLITE.HQX (U) Compression/decompression/binhex program v3.0.5 (R. Lau) [/pub/software/mac/stuffitlite.hqx or stuffitlite.sea] TOPPPRED.HQX (N) Prediction of transmembrane segments and their topology (G. v. Heijne, M.G. Claros) YEASTSTRAINS.HQX (U) Strain management, in particular yeast v1.2 (K. Froehlich) [/pub/software/mac/yeaststrains.hqx] UNIX: ----- BLKSRCH.UUE (N) Block search analysis of protein sequences with the BLOCKS database (R. Fuchs) [/pub/software/unix/blocksearch.tar.Z] BTAB.UAA (N) BLAST output parser (M. Dubnick) [/pub/software/unix/btab.tar.Z] double-digester.tar.Z (N) Graphical analysis of double digest restriction (only on FTP server) data (L. Wright). DTASK11S.UAA (N) Smith-Waterman database searches on parallel work- stations (G. Hauge) [/pub/software/unix/dtask11s.tar.Z] FILTER.UAA (U) Suboptimal alignments and motif recognition (P. Argos) [/pub/software/unix/filter.tar.Z] GENAL.UUE (N) Alignments of genomic sequences with coding regions (J. Stoevlbaek) [/pub/software/unix/genal.tar.Z] GM.UAA (U) Analysis of unknown DNA sequences v2.0 (C. Fields) [/pub/software/unix/gm.tar.Z] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/unix/hth.c] MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers v3.1 (T. deBoer) [/pub/software/unix/mailfasta.tar.Z] MOLBIO.UAA (N) C++ clas library for molecular biology (K. Robison) [/pub/software/unix/molbio.tar.Z] RASMOL.UAA (N) Visualisation of macromolecules using PDB files (R. Sayle) [/pub/software/unix/rasmol.tar.Z] READSEQ.UAA (U) Sequence format conversion program (D. Gilbert) [/pub/software/unix/readseq.tar.Z] SUPER.UAA (N) Tool for electronic user polls (R. Doelz) [/pub/software/unix/super.tar.Z] VAX: ---- BLKSRCH.UUE (N) Block search analysis of protein sequences with the BLOCKS database (R. Fuchs) [/pub/software/vax/blksrch.uue] FILTER.UAA (U) Suboptimal alignments and motif recognition (P. Argos) [/pub/software/vax/filter.uaa to filter.uad] GCGMENU.UAA (N) Menu interface to GCG package (C. Gartmann) [/pub/software/vax/gcgmenu.uaa and gcgmenu.uab] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/vax/hth.c] PDBTOGCG.FOR (N) Extracts protein sequences from PDB files (M. Mezei) [/pub/software/vax/pdbtogcg.for] READSEQ.UAA (U) Sequence format conversion program (D. Gilbert) [/pub/software/vax/readseq.uaa to readseq.uac] SUPER.UUE (N) Tool for electronic user polls (R. Doelz) [/pub/software/unix/super.uue] TFD2GCG.FOR (N) Converts TFD SITES table to GCG Prosite format (D. Mathog) [/pub/software/vax/tfd2gcg.for] UNZIP.UUE (N) Decompresses ZIP encoded files (H. Smith) [/pub/software/vax/unzip.uue] <5> 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: o DS13648.DAT - Alignment of plasmodial small subunit rRNAs. Submitted by V.Enea, 26-Feb-1993 o DS13893.DAT - Alignment of amino acid sequences derived from conceptual reading frames of Tc1-like elements from fish, nematodes, fruit flies an agnathan, and a spider. Submitted by D.H.A. Fitch, 18-Mar-1993 o DS13894.DAT - Alignment of Tc1-like elements from salmon, trout, zebrafish, and catfish. Submitted by D.H.A. Fitch, 18-Mar-1993 o DS14642.DAT - Alignment of amino acid sequences of the zinc-containing long-chain alcohol dehydrogenases. Submitted by S. Yokoyama, 17-Jun-1993 <6> 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. 35, Jun 93 + updates) * Eukaryotic Promotor Database /pub/databases/epd EPD (Rel. 35, May 93) * SwissProt Protein Sequence Database /pub/databases/swissprot PROT (Rel. 25, Apr 92 + updates) * Prosite pattern database /pub/databases/prosite PROSITE (Rel. 10.1, Apr 93) * ENZYME database /pub/databases/enzyme ENZYME (Rel. 12.00, Aug 93) * Brookhaven Protein Databank not available PROTEINDATA (Rel. 61, Jul 92 + pre-release) * REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE (Rel. 9307, Jul 93) * RELIBRARY, Restriction Enzyme List /pub/databases/relibrary RELIBRARY (Apr 1993) * tRNA sequence and gene sequence db /pub/databases/trna TRNA (1993) * REPBASE - Prototypic sequences for /pub/databases/repbase REPBASE human repetitive DNA (Rel. 1.01 1992) * TFD, Transcription Factor Database /pub/databases/tfd TFD (Ver 5.5, Nov 92) * ECD, E.coli Database /pub/databases/ecd ECD (Rel. 14, Feb 93) 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. 38, Apr 93) 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, Oct 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 (Jun 1993) CUTG, codon usage /pub/databases/cutg CUTG tabulated from GenBank rel. 69 * 3D_Ali, 3D alignment database /pub/databases/3d_ali 3D_ALI (Jun 1993) * RLDB, Reference Library Database /pub/databases/rldb (Jun 1993) (ftp only) * PKCDD, Protein Kinase Catalytic /pub/databases/pkcdd PKCDD Domain Database (April 1993) * CpG Islands Database /pub/databases/cpgisle CPGISLE (Release 2.0, Apr 1992) * Blocks database /pub/databases/blocks BLOCKS (Rel. 6.0, Jan 1993) * HLA, Alignments of human HLA /pub/databases/hla HLA sequences (Jul 1993) * TRANSTERM, Translational /pub/databases/transterm TRANSTERM Termination Signal Database (Apr 1993) * LISTA, Yeast coding sequences /pub/databases/lista LISTA (Rel. 2.0, Apr 1993) * 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 (Sep 1992) (ftp only) pdb_select Misfolded, database of deliberately /pub/database/protein_extras/misfolded misfolded protein models (Nov 92) (ftp only) 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 * Crystallographers' information /pub/databases/xray XRAY <7> 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. <8> Network addresses at EMBL ------------------------- EMBL File Server (e-mail requests) NetServ@EMBL-Heidelberg.DE Anonymous FTP FTP.EMBL-Heidelberg.DE BLITZ e-mail server Blitz@EMBL-Heidelberg.DE FASTA e-mail server FASTA@EMBL-Heidelberg.DE Quicksearch e-mail server Quick@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