NETHELP@embl.bitnet (02/12/91)
------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 3, February 12th 1990 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | E-mail: NetHelp@EMBL.bitnet Tel: +49 6221 387258 | | NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 or 387306 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Updates to existing 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 Existing Data Collections ------------------------------------ The following data collections have been updated recently: REBase - Release 9102 February 1991, of Rich Robert's restriction enzyme database. Enzyme - Release 3.1 of Amos Bairoch's enzyme database. RefList - Release 14.0 of Amos Bairoch's SeqAnalRef database. TFD - Release 2.1 of David Ghosh's transcription factor database The directory NUC is continually updated with nucleotide sequence data from EMBL/GenBank/DDBJ, and the directory PROT is updated with data from the SWISS-PROT protein sequence database. <3> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): DOS: ---- SIM.UUE (N) Program for detecting local sequence similarities (G. Huang and W. Miller) TFD2PROSITE.C (N) Conversion utility to transform the TFD sites table to Prosite format (R. Fuchs) COSY.UAA (U) Replacing a defect archive on the server. A package for enzyme kinetics calculations (M. Eberhard) CREGEX.C (U) v1.1 of J. Leunissens program to convert Prosite to Prosearch format PROSEA12.UAA (U) v1.2 of L. Kolakowski's program to search patterns in protein sequences using the Prosite database Mac: ---- MACTARGSEARCH.HQX (N) Program to search DNA sequences with sequence profiles (J.A. Goodrich, W.R. McClure, M.L. Schwartz) SEQLOGO.HQX (N) Graphical representation of sequence patterns by "sequence logos" (T. Schneider) TFD2PROSITE.C (N) Conversion utility to transform the TFD sites table to Prosite format (R. Fuchs) DNATRANSLATOR.HQX (U) Update (v.0.97.3) to D.J. Eernisse's HyperCard stack for phylogenetic analyses MACPATTERN.HQX (U) Update (v1.2.3) to R. Fuchs's program for pattern searching using Prosite Unix: ----- TFD2PROSITE.C (N) Conversion utility to transform the TFD sites table to Prosite format (R. Fuchs) CREGEX.C (U) v1.1 of J. Leunissens program to convert Prosite to Prosearch format PROSEARCH.UAA (U) v1.2 of L. Kolakowski's program to search patterns in protein sequences using the Prosite database SEQF.UAA (N) Programs for searching genetic sequence databases (D. Davison and M. Kanehisa) VAX: ---- SIM.UUE (N) Program for detecting local sequence similarities (G. Huang and W. Miller) TFD2PROSITE.C (N) Conversion utility to transform the TFD sites table to Prosite format (R. Fuchs) CREGEX.C (U) v1.1 of J. Leunissens program to convert Prosite to Prosearch format PROSEARCH.UAA (U) v1.2 of L. Kolakowski's program to search patterns in protein sequences using the Prosite database <4> Other updates ------------- DOC - BIOSCI.DOC January 1991 version of the BIOSCI bulletin-board description. - GEPSAN.1 Issue 1 of the Geneva Protein Sequence Analysis Newsletter, by Amos Bairoch, University of Geneva RefList - FANS_REF Functional analysis of nucleotide sequences bibliography, by M.S. Gelfand, USSR Academy of Sciences. <5> Summary of Directories of the EMBL File Server ------------------------------------------- Summary of directories available on the EMBL File Server: Databases: EMBL Nucleotide Sequence Database NUC (Rel. 25, Nov 90 + new data from EMBL/GenBank/DDBJ) Eukaryotic Promotor Database (Rel. 25, Nov 90) EPD SwissProt Protein Database (Rel. 16, Oct 90) PROT ProSite pattern database (Rel. 6.0, Nov 90) PROSITE ENZYME database (Rel. 3.1, Feb 91) ENZYME Brookhaven Protein Structure Database (Rel. 54, Nov 90) PROTEINDATA REBASE, Restriction Enzyme Database (Rel. 9102, Feb 91) REBASE TFD, Transcription Factor Database (Ver 2.1, Feb 91) TFD The E.coli Database (Rel. 5, Nov 90) ECD Drosophila Genetic Map Database (Rel. 3.5, Aug 90) DROSOPHILA Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB Sequence analysis bibliography (SEQANALREF Rel. 14.0, Feb 91) REFLIST Functional Analysis of Nucleotide Sequences bibliography REFLIST (FANS_REF Rel. 1.3, Nov 90) 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 either of the addresses: NetServ@EMBL.bitnet 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.