Version 4.3 available for all Unix systems by anonymous ftp at :-
In the UK ftp.sanger.ac.uk/pub/acedb/ace4_3/ (NOTE No version 4.3 for Linux here)
In the US ncbi.nlm.nih.gov/repository/acedb/ace4_3/
In France lirmm.lirmm.fr/pub/acedb/ace4_3/ (NOTE No version 4.3 for Linux here)
In Israel bioinformatics.weizmann.ac.il/pub/databases/acedb/ace4_3/ (NOTE No version 4.3 for Linux here)
In the US ncbi.nlm.nih.gov/repository/acedb/ace4_3/
In the UK ftp.ebi.ac.uk/pub/databases/parasites/bin/
MacAce 2 and MacAce4.04b (a beta release) as "standalone" or "empty" versions are available at the same sites in both a PowerPC version and a "fat" binary version for 030/040 Macs
available by anonymous ftp at
(NOTE The updates are now subdivided into one set (update.WG1.4-1.tar.Z etc.) without the full nucleotide data and another set (update.WS1.4-1.tar.Z etc.) with nucleotide data. The former set is currently (10/10/96) at release 4-6 whereas the latter (much much larger in size) is at release 4-20. The method for uploading and installing remains the same however - although version 4_3 of the ACEDB code should be used.)
There is a new version of the C. elegans ACEDB database. This uses version 4_0 of the ACEDB code (subversion beta4). There will be a separate email message about the code for those using ACEDB for other organisms. To build the C. elegans database you will need to get all six update files update.4-1.tar.Z to update.4-6.tar.Z.
The total database size is now approximately 160Mbytes. As well as a large amount of new sequence data, this contains all the genetic mapping data submitted to the CGC in Cambridge up to April 1995, together with a draft new map, and the abtracts for the 1995 Worm Meeting with links to Gene, Rearrangement and Sequence objects.
This release is fully up to date with respect to the physical map, the CGC information, and gene/genetic map information prior to that resulting from the recent call for data (which we are working on now). We have also added over 200 Medline references and a significant number of missing Gazette pages. There is also a lot of new genomic sequence information.
Instructions for obtaining updates/the whole thing
All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet:
in the USA, in repository/acedb/celegans
and from
in England, in pub/acedb/celegans
lirmm.lirmm.fr (193.49.104.10)
in France, in directory genome/acedb/celegans
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 email address'
cd repository/acedb/ace4
binary
mget *
get README y/n answer yes etc
...
...
quit
Get all the update.4-n.tar.Z and read the files README and 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") and 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.
Please send any comments, especially about anything you think is wrong to one of us:
Richard Durbin (rd@sanger.ac.uk) Sylvia Martinelli (sylvia@sanger.ac.uk)
Recommended literature :-