NETHELP@EMBL-HEIDELBERG.DE (06/26/91)
------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 5, June 26th 1991 | | | | 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> Updates to data collections <3> Updates to software collection <4> Other updates <5> Summary of contents of file server <6> Getting started ? <1> Introduction ------------- 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.2). <2> Updates to Data Collections ------------------------------------ tRNA - We have added a compilation of tRNA sequences from Mathias Sprinzl at the University of Bayreuth, Germany. The database files are located in the file server directory TRNA. Sprinzl M., Dank N., Nock S., Schon A. (1991) Nucl. Acids Res. 19, Supplement, 2127-. PROTEINDATA - A database of homology-derived protein secondary structures (HSSP) has been added, supplied by Chris Sander and Reinhard Schneider (Protein Design Group, EMBL). The database is a merger of 3-D structure information from the Protein Data Bank (PDB) and sequence information from SwissProt (see Proteins 9, 56-68 (1991)). There is one file for each PDB protein containing all protein sequences deemed homologous to this protein, in the form of multiple sequence alignments. Example: get PROTEINDATA:1PPT.HSSP (for pancreatic polypeptide ) The DSSP database of secondary structures has been extended by extracting secondary structure assignments for 28 proteins for which only C(alpha) coordinates have been deposited. This was done with the aid of a model building proc edure that adds backbone coordinates to a C(alpha) trace (L.Holm and C.Sander, J.Mol.Biol. 218, 183-194 (1991)). Example: get PROTEINDATA:3p21.dssp_ca (for p21 ras) Use DIR PROTEINDATA command to get for more information about PDB, DSSP and HSSP-related data files and programs. 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: ---- PROGRAPH.UAA (N) Protein sequence analysis package (K. Hoffmann) CUTCOST.UAA (U) Program to determine the cheapest source for restriction enzymes v2.31 (C.G. Meinhof) Mac: ---- Plota protein sequence analysis package (A. Luttke, P. Markiewicz) (N) PLOTA_AADATA.HQX Sequence editor PLOTA_DOT.HQX Dot matrix comparison PLOTA_GGR.HQX Secondary structure prediction PLOTA_GOR.HQX Secondary structure prediction PLOTA_HEL.HQX Helical wheel PLOTA_HYD.HQX Hydropathy analysis PLOTA_HYD5.HQX Hydropathy analysis (averaging) PLOTA_KAS.HQX Chain flexibility and antigenicity PLOTA_KKD.HQX Prediction of membrane spanning regions PLOTA_POW.HQX Power spectrum plot PLOTA_SIG.HQX Signal peptide prediction PLOTA_SIM.HQX Dissimilarity plot PLOTA_TMH.HQX Hydrophobic moment analysis DBCONV.HQX (N) Tool for reformatting "line-type" databases to tab-delimited format (J.R. Valverde) EMBL-SEARCH.HQX (N) Simple database retrieval program demonstrating the use of the EMBL CD-ROM indices (R. Fuchs) SEQSPEAK.HQX (N) Sequence data entry with acoustic feedback (K. Conover) TRNA-SEARCH.HQX (N) Identification of tRNA genes and plotting of RNA structure (R.D. Shortridge) DNATRANSLATOR.HQX (U) Version 0.99.1 of the phylogenetic analysis HyperCard stack (D.J. Eernisse) MACMOLECULE.HQX (U) 3D models of biomolecules v1.5 (E. Myers et al.) MACPATTERN.HQX (U) Protein pattern searching with Prosite, v1.2.5 (R. Fuchs) MACTARGSEARCH.HQX (U) Program to search DNA sequences with sequence profiles v2.0 (J.A. Goodrich, W.R. McClure, M.L. Schwartz) UNIX: ----- HOMOCHART.UUE (N) Nice plotting of multiple alignments (R. Smith) OVERSEER.UUE (N) Nucleic acid sequence database analysis package (P. Sibbald) VAX: ---- BOXSHADE.UUE (N) Nice plotting of multiple aligments (K. Hoffmann) DBCONV.HQX (N) Tool for reformatting "line-type" databases to tab-delimited format (J.R. Valverde) OVERSEER.UUE (N) Nucleic acid sequence database analysis package (P. Sibbald) SCRUTINE.UAA (U) Scrutineer protein sequence database analysis package, version May 1991 (P. Sibbald) <4> Other updates ------------- DOC - BIOSCI.DOC April 1991 version of the BIOSCI bulletin-board description. - ORDERFORM.TXT EMBL Data Library subscription form 1991/2 - ORDERINFO.TXT EMBL Data Library subscription information for 1991/2 - CDROM_INDEX.HQX Description of binary indices provided on current EMBL CD-ROMs for access to sequence database files. This is a Macintosh MS Word 4.0 document compressed and converted to ascii by Stuffit. ALIGN - DS6900.UUE Alignment of pseudoeta-globin genes and surrounding sequences from primates and goat. by W. Bailey, Wayne State Univ, Detroit. <5> Summary of Directories of the EMBL File Server ------------------------------------------- Databases (* = new or updated): * EMBL Nucleotide Sequence Database NUC (Rel. 27, May 91 + new data from EMBL/GenBank/DDBJ) * Eukaryotic Promotor Database (Rel. 27, May 91) EPD * SwissProt Protein Database (Rel. 18, May 91) PROT * Prosite pattern database (Rel. 7.00, May 91) PROSITE * ENZYME database (Rel. 5, May 91) ENZYME Brookhaven Protein Structure Database (Rel. 54, Nov 90) PROTEINDATA * REBASE, Restriction Enzyme Database (Rel. 9106, Jun 91) REBASE * tRNA sequence and gene sequence database (1991) TRNA * TFD, Transcription Factor Database (Ver 3.0, Jun 91) TFD * The E.coli Database (Rel. 7, May 91) ECD Drosophila Genetic Map Database (Rel. 9012, Dec 90) DROSOPHILA Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB * Sequence analysis bibliography (SEQANALREF Rel. 17, Jun 91) REFLIST * Functional Analysis of Nucleotide Sequences bibliography REFLIST (FANS_REF Rel. 3.4, Apr 91) Alu sequence database and alignment ALU 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: NetServ@EMBL-Heidelberg.DE containing just the word HELP on a line by itself. No essays please. For human contact, send electronic mail to NetHelp at the address(es) given above.