From owner-celegans@net.bio.net Sat Sep 21 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.celegans Subject: ACEDB data updates for C.elegans Date: 22 Sep 1996 05:12:38 +0100 Lines: 101 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <522ebm$aks@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates WG1.4-6 and WS1.4-17 to 4-20 for C. elegans ============================================================= You should be using these in conjunction with release 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS1 update series contains everything, whereas WG1 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG1.4-5 and WS1.4-16 are: for both types of update - a physical map update with a few changes (mid Sept) - accumulated genetic data including new gene_classes, loci and mapping data - expression data from 2 new labs, Naples and Strasbourg. - some old Cell mistakes have been corrected and for just the complete database including sequences (WS1.4-20) Data fom St Louis and Sanger Sequence databases taken in mid-Sept: - There are now 1714 (1586 before) cosmids totalling 51,655,842 (47,908,858 before) bases. - We are switching from using the PIR protein database for homology searches to the TREMBL database, hence many PIR homologies are being deleted and TR ones added. The total database sizes after adding these updates are around 390Mb for the WS1 database (we said it would grow!) and around 65Mb for the WG1 database. It will take a long time to read in the WS1 updates, particularly WS1.4-19. All four updates took us several hours. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_3.tar.Z # get program cd ../celegans # change to worm data directory mget update.WS1.* # get all WS1 update files quit -------------------------------- Get any update files that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- .