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ACEDB data updates WG2.4-3 to 4-4 and WS2.4-17 to 4-20 for C. elegans
You should be using these in conjunction with release 4_3 of the acedb
**** WARNING ****
Unfortunately, these update files increase the WS2 database size on disk
to around 700Mb. We have been trying to find a way to reduce this,
which has led to the delay in this release. We plan to make another
release before the Madison Worm Meeting (May 28 - June 1), and hope
that will use less disk space.
Reminder: there are now two versions of the C.elegans database. The
WS2 update series contains everything, whereas WG2 update series
contains all data except sequences and directly related material
(proteins, motifs etc.), for those with limited resources.
The additions since WG2.4-2 and WS2.4-16 are:
for both types of update
- a fix to the map displays which were behaving oddly
- the expression pictures with the display script from
wscripts/ that was missing in the initial WS/G2 release.
(the next update will have bibliography, genetics, embl etc
and for just the complete database including sequences (WS2.4-17 plus)
Data fom St Louis and Sanger Sequence databases taken in mid-Apr:
- There are now 2177 ( 2020 before) cosmids totalling 65222006
(60615799 before) bases.
- Peptides have been updated only to include new ones.
The total database sizes after adding these updates are around 700Mb
for the WS2 database and around 65Mb for the WG2 database.
It will take time to read in the WS2 updates, perhaps 2-3 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 (184.108.40.206) in the USA, in repository/acedb
ftp.sanger.ac.uk (220.127.116.11) in England, in pub/acedb
lirmm.lirmm.fr (18.104.22.168) 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.
password: your user id or email address
cd repository/acedb # change to relevant directoy
binary # IMPORTANT
dir # display files in this directory
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
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 at sanger.ac.uk).
Comments about the program, or the installation procedure, should be
sent to one of us:
Richard Durbin (rd at sanger.ac.uk)
Jean Thierry-Mieg (mieg at kaa.cnrs-mop.fr)
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