EMBL File Server News: Number 7, January 1st 1992
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From bronze!news.cs.indiana.edu!bionet!EMBL-HEIDELBERG.DE!NETHELP Thu Jan 2 16:33:17 EST 1992 Article: 57 of bionet.molbio.embldatabank Path: bronze!news.cs.indiana.edu!bionet!EMBL-HEIDELBERG.DE!NETHELP From: [email protected] Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server News: Number 7, January 1st 1992 Message-ID: <[email protected]> Date: 1 Jan 92 23:23:00 GMT Sender: [email protected] Distribution: bionet Lines: 196 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 7, January 1st 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> Updates to data collections <3> Updates to software collection <4> Other updates <5> Summary of directories on the file server <6> Getting started ? <1> Introduction ------------- REMINDER: EMBL has withdrawn from the BITNET/EARN computer network as from today. Use only the Internet address, [email protected] The old address, [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 server (eg. GET DOC:EMBL_Server_News.5). <2> Updates to Data Collections ------------------------------------ Two new databases have been added to the file server recently: (a) The Haemophilia B database, provided by Professor Gordon Brownlee, University of Oxford, is available in the file server directory: HAEMB Giannelli F., Green P.M., High K.A. et.al. "Haemophilia B: database of point mutations and short additions and deletions - second edition" Nucleic Acids Res. 19:2193-2219 (1991). For more information send the command HELP HAEMB. (b) A compilation of small RNA sequences, provided by Ram Reddy, Baylor College of Medicine, Houston, is available in the file server directory: SMALLRNA Gupta S., Reddy R. "Compilation of Small RNA Sequences" Nucleic Acids Res. 19:2073-2075 (1991). For more information send the command HELP SMALLRNA. Just about every existing collection has been updated since the last newsletter so we will not detail them here. The current versions of all collections are detailed below. <3> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): DOS: ---- CM.UAA (N) Graphically oriented restriction map construction from multiple digestion data (K. Hoffmann) MARKER.UUE (N) Creation of restriction fragments banding patterns and DNA length standards (S. Rensing) PROGRAPH.UAA (U) Graphically oriented protein sequence analysis package (K. Hoffmann) Mac: ---- ALIGN.HQX (N) Feng and Doolittle's sequence alignment and phylogeny programs (ported by P. Markiewicz) STRAINCOLLECTION.HQX (N) HyperCard stack for bacterial strain management (D. Moore) MACPATTERN.HQX (U) Protein pattern searching with Prosite, v1.5 (R. Fuchs) READSEQ.HQX (U) Sequence format conversion program, Nov 1991 (D. Gilbert) UNIX: ----- READSEQ.UUE (U) Sequence format conversion program, Nov 1991 (D. Gilbert) VAX: ---- ACCESS.UUE (N) GCG tool for extracting entries from the database (J. Prilusky) BLAST.UAA (N) NCBI's fast database searching programs BLASTINC.UUE (VMS version by P. Stockwell) BLASTLIB.UAA BLASTVMS.UAA BLASTSEARCH.TXT (N) DCL script for using GenBank's BLAST server (S. Clark) EASYMENU.UUE (N) Menu interface to the GCG package (J. Prilusky) SEQCOMP.TXT (N) Analysis of peptide composition in a protein sequence (P. Dessen) FASTEMBL.COM (U) Script for using the EMBL Mail-Fasta server (for GCG 7) (E. Sonnhammer) MALIGNED.UAA (U) Multiple sequence editor, v1.64 (S. Clark) PRETTYBOX.TXT (U) Pretty formatting of multiple sequence alignments, v1.1 (R. Westerman) READSEQ.UAA (U) Sequence format conversion program, Nov 1991 (D. Gilbert) SCRUTINE.UAA (U) Protein database analysis program, Nov 1991 (P. Sibbald) <4> Other updates ------------- ALIGN directory: DS8841 - alignment of epsilon globin gene sequences from 17 eutherian mammals, provided by Wendy Bailey and Morris Goodman, Wayne State University. <5> Summary of directories on the file server --------------------------------------- Databases (* = new or updated since 25-Sep-91) *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. 9112, Dec 91) 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 (9111, 10-Nov-91) 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 91) HAEMB *Compilation of small RNA sequences (Oct 91) SMALLRNA 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 <6> Getting Started ? ----------------- The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail. The service is free. For initial information, send standard electronic mail to the address: [email protected] containing just the word HELP on a line by itself. No essays please. For human contact, send electronic mail to NetHelp at the address given above.