Difference between revisions of "EMBL File Server News, No. 8 June 25th 1992"
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From bronze!sol.ctr.columbia.edu!ucselx!bionet!EMBL-HEIDELBERG.DE!NETHELP Thu Jun 25 07:51:53 EST 1992 Article: 75 of bionet.molbio.embldatabank Path: bronze!sol.ctr.columbia.edu!ucselx!bionet!EMBL-HEIDELBERG.DE!NETHELP From: [email protected] Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server News, No. 8 June 25th 1992 Message-ID: <[email protected]> Date: 25 Jun 92 12:10:00 GMT Sender: [email protected] Distribution: bionet Lines: 432 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 8, June 25th 1992 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: [email protected] Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Anonymous FTP server <3> Gopher server <4> Updates to data collections <5> Updates to software collection <6> Other updates <7> Summary of directories on the file server <8> Getting started ? <9> Network addresses at EMBL <10> Footnotes <1> Introduction ------------- The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail or anonymous FTP. The service is free. <2> Anonymous FTP server -------------------- An anonymous FTP server is now operational at the internet address FTP.EMBL-Heidelberg.DE (188.8.131.52) Users should log in with the username "anonymous", and for the password give their e-mail address. The FTP archive currently contains molecular biology databases, free molecular biology software and other files similar to the facilities offered by the e-mail server ([email protected]). Weekly batches of additions to the EMBL nucleotide sequence database (data from EMBL/GenBank/DDBJ) are made available as compressed tar files in the directory: /pub/databases/embl/new Individual sequence database entries are not available via FTP: we recommend use of the e-mail server for this purpose. <3> Gopher server ------------- A gopher server is available as part of an experimental network of EMBnet gopher sites, providing access to the EMBL FTP archive and to other "Biogophers" in Europe, Israel and the USA. Gopher clients should connect to FTP.EMBL-Heidelberg.DE at port 70. Administrators of other Gopher servers may add the following link information: Name=EMBnet BioInformation Resource EMBL Type=1 Port=70 Path=1/ Host=ftp.embl-heidelberg.de <4> Updates to Data Collections ------------------------------------ Two new databases have been added to the file server recently: (a) The Reference Library Database system (RLDB) provided by Guenther Zehetner, Genome Analysis Laboratory, ICRF, London. E-mail server: directory RLDB Anonymous ftp: /pub/databases/rldb (b) A database of 3-D alignments (3D_ALI) provided by Stefan Pascarella and Pat Argos, EMBL. Pascarella S., Argos P. "A data bank merging related protein structures and sequences" Protein Engineering 5 (1) 121-137 (1992). E-mail server: directory 3D_ALI Anonymous ftp: /pub/databases/3d_ali <5> 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: ---- DNAFRAG.UUE (N) Measures molecule size of gel bands from standards (J. Nash) [/pub/software/dos/dnafrag.uue] GEL-JML.UAA (N) Calculation of DNA restriction fragment sizes (J.M. Lacroix) [/pub/software/dos/gel-jml.uaa and gel-jml.uab] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/dos/gmd.txt] MACAW103.UAA (N) Multiple sequence editor (G. Schuler) [/pub/software/dos/macaw103.uaa to macaw103.uac] MARKER.UUE (U) Creation of restriction fragments banding patterns and DNA length standards v1.1 (S. Rensing) [/pub/software/dos/marker.uue] MISMATCH.TXT (N) Selection of PCR designed mismatch primers (L.S. Davidow) [/pub/software/dos/mismatch.txt] NUMCLONE.UUE (N) Estimates the number of clones one has to screen from a genomic library in order to find a desired clone (J. Nash) [/pub/software/dos/numclone.uue] PRIMGEN.UUE (N) Oligonucleotide primer design by reverse-translation of amino acid sequences (J. Nash) [/pub/software/dos/primgen.uue] PRNTGL.UAA (U) Prints HGPL files on matrix of laser printer v1.18 (C. Ravitz) [/pub/software/dos/prntgl.uaa and prntgl.uab] SIM.UUE (U) Local similarity searching (G. Huang) [/pub/software/dos/sim.uue] SSCAN.UAA (U) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/dos/sscan.uaa to scan.uad] Mac: ---- ALIGNER.HQX (N) Multiple sequence editor (D. Eernisse) [/pub/software/mac/aligner.hqx] AMPLIFY.HQX (N) Tools for PCR primer checks (B. Engels) [/pub/software/mac/amplify.hqx] DNAID.HQX (U) DNA sequence editor and analysis program v1.6 (F. Dardel) [/pub/software/mac/dnaid.hqx] EMBL-SEARCH.HQX (N) Database retrieval software for EMBL CD-ROM (R. Fuchs) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (N) Source code for EMBL-Search v2.0 [/pub/software/mac/embl-search_src.hqx] GBSEARCH.HQX (U) Tool to assist access to GenBank server (D. Gilbert) [/pub/software/mac/gbsearch.hqx] GENEWORKS_DEMO.HQX (N) Demo version of IG's sequence analysis package [/pub/software/mac/geneworks_demo.hqx] GENE_JOCKEY_DEMO.HQX (N) Demo version of Biosoft's sequence analysis package [/pub/software/mac/gene_jockey_demo.hqx] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/mac/gmd.txt] MACMIMIC_DEMO.HQX (N) Demo version of Instar's molecular modelling package [/pub/software/mac/macmimic_demo.hqx] MACMOLECULE.HQX (U) 3d models of biomolecules v1.7 (E. Myers) [/pub/software/mac/macmolecule.hqx] MACPATTERN.HQX (U) Protein pattern searching with Prosite, v1.6.2 (R. Fuchs) [/pub/software/mac/macpattern.hqx] MACSIGNALSCAN.HQX (N) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/mac/macsignalscan.hqx] MACVECTOR_DEMO.HQX (N) Demo of IBI's sequence analysis package [/pub/software/mac/macvector_demo.hqx] SIGNALASE.HQX (N) Analysis of mammalian signal peptide sequences (N. Matei) [/pub/software/mac/signalase.hqx] UNIX: ----- BLAST.UAA (U) Fast sequence database searching [/pub/software/unix/blast.tar.Z] DFA.UAA (U) Required by BLAST.UAA [/pub/software/unix/dfa.tar.Z] FILTER.UAA (N) Set of programs for suboptimal alignments ans recognition of reliably aligned sequences (P. Argos) [/pub/software/unix/filter.tar.Z] GCI.UAA (N) A network server for interactive 3D graphics (G. Tuparev) [/pub/software/unix/gci.tar.Z] GISH.UUE (U) Required by BLAST.UAA [/pub/software/unix/gish.tar.Z] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/unix/gmd.txt] MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers v2.1 (T. deBoer) [/pub/software/unix/mailfasta.tar.Z] NCBI.UAA (U) Required by BLAST.UAA [/pub/software/unix/ncbi.tar.Z] PIMA.UAA (U) Pattern-induced multi-sequence alignments v1.22 (R.F. Smith) [/pub/software/unix/pima.tar.Z] PLSEARCH.UAA (U) Pattern detection in proteins v4.2 (R.F. Smith) [/pub/software/unix/plsearch.tar.Z] READSEQ.UUE (U) Sequence format conversion program, Apr 1992 (D. Gilbert) [/pub/software/unix/readseq.tar.Z] SIGSCAN.UAA (U) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/unix/sigscan.tar.Z] SIM.UUE (U) Local similarity searching (G. Huang) [/pub/software/unix/sim.tar.Z] VAX: ---- BLASTMAIL.COM (N) DCL script for using GenBank's BLAST server (E.L. Sonnhammer) [/pub/software/vax/blastmail.com] FASTEMBL.COM (U) Script for using the EMBL Mail-Fasta server (for GCG 7), v 1.w (E. Sonnhammer) [/pub/software/vax/fastembl.com] FILTER.UAA (N) Set of programs for suboptimal alignments ans recognition of reliably aligned sequences (P. Argos) [/pub/software/vax/filter.uaa to filter.uac] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/vax/gmd.txt] INTERFACE.UUE (N) Pascal programming interface for GCG package (J. Prilusky) [/pub/software/vax/interface.uue] MALIGNED.UAA (U) Multiple sequence editor, v1.65b (S. Clark) [/pub/software/vax/maligned.uaa to maligned.uad] READSEQ.UAA (U) Sequence format conversion program, Apr 1992 (D. Gilbert) [/pub/software/vax/readseq.uaa and readseq.uab] SCRUTINE.UAA (U) Scrutineer, sequence database analysis, Jun 1992 (P. Sibbald) [/pub/softare/vax/scrutine.uaa] SIM.UUE (U) Local similarity searching (G. Huang) [/pub/software/vax/sim.uue] SSCAN.UAA (U) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/vax/sscan.uaa to sscan.uac] <6> Other updates ------------- ALIGN directory: o DS10014.DAT - Alignment of exon 1 of the interphoto- receptor binding protein (IRBP) gene. Submitted by J. Stanhope, 4-Feb-1992. o DS10763.DAT - Alignment of duplicated gamme globin gene sequences from mammals. Submitted by W. Bailey, 24-Apr-1992. o DS10819.DAT - Alignment of potassium channel gene family. Submitted by M. Strong, 13-May-1992 o DS10830.DAT - Alignment of potassium channel genes, Shaw related gene family. Submitted by M. Strong, 14-May-1992 o DS10831.DAT - Alignment of S4 segment of Na+,Ca++, and K+ ion channel genes. Submitted by M. Strong, 14-May-1992 o DS10832.DAT - Alignment of potassium channel genes, Shaker related gene family. Submitted by M. Strong, 13-May-1992 o DS10833.DAT - Alignment of sodium channel gene family. Submitted by M. Strong, 13-May-1992 <7> Summary of directories on the file server --------------------------------------- Anonymous ftp NetServ -------------- --------- EMBL Nucleotide Sequence Database /pub/databases/embl NUC (Rel. 31, Jun 92 + updates) Eukaryotic Promotor Database /pub/databases/epd EPD (Rel. 31, May 92) SwissProt Protein Sequence Database /pub/databases/swissprot PROT (Rel. 22, May 92 + updates) Prosite pattern database /pub/databases/prosite PROSITE (Rel. 9.00, Jun 92) ENZYME database /pub/databases/enzyme ENZYME (Rel. 9.00, May 92) Brookhaven Protein Databank not available PROTEINDATA (Rel. 58, Oct 91) REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE (Rel. 9206, Jun 92) tRNA sequence and gene sequence db /pub/databases/trna TRNA (1991) TFD, Transcription Factor Database /pub/databases/tfd TFD (Ver 4.3, Mar 92) ECD, E.coli Database /pub/databases/ecd ECD (Rel. 11, Jun 92) FLYBASE, Drosophila Genetic Map db /pub/databases/flybase FLYBASE (9206, 1-Jun-1992) LiMB, Listing of Mol. Biol. db's /pub/databases/limb LIMB (Rel. 2.0) SEQANALREF, Seq. analysis refs /pub/databases/reflist REFLIST (Rel. 28, Jun 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 (Dec 1991) 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 (1991) 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) 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 <8> Getting Started ? ----------------- For initial information, send standard electronic mail to the address: [email protected] 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. <9> Network addresses at EMBL ------------------------- EMBL File Server (e-mail requests) [email protected] FASTA e-mail server [email protected] Quicksearch e-mail server [email protected] Anonymous FTP FTP.EMBL-Heidelberg.DE Problems, feedback (human contact) [email protected] EMBL Data Library enquiries [email protected] EMBL Data Library sequence submissions [email protected] Software submissions and problems [email protected] <10> Footnotes --------- REMINDER: EMBL has withdrawn from the BITNET/EARN computer network. Use only the Internet address, eg [email protected] The old address, eg [email protected], is terminated. The EMBL File Server Newsletter summarises changes to the EMBL File Server. This newsletter and older issues are available from the mail server (eg. GET DOC:EMBL_Server_News.7), or via anonymous ftp in the directory /pub/doc