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New ACEDB data release WG2.4-2 and WS2.4-16 for C. elegans
With this release we are starting a new series of database updates
from scratch again, rather than adding on to WS1.4-30. The new series
is called WS2 (and correspondingly WG2 for the version without
Because we are restarting from scratch, you must get all the updates
from the series you want (WS2 or WG2), and rebuild a new database
using them. Fortunately, it will be much faster reading in the
sixteen new WS2 updates than thirty-some of the WS1 series.
If you have a working acedb version built with the WS1 series, you
must do two things:
(1) you must remove your current database/ directory (ideally after
backing it up in case of difficulties). As well as removing the
database directory, you can also remove any update.WS1...tar.Z or
(2) you must get a new copy of the INSTALL script, as well as all
the new WS2 updates.
If you do not remove the contents of the database directory, when
you start up acedb it will still say "WS1" in the title bar, and will
not be able to load the WS2 updates. When you have emptied it
properly, it will ask if you want to reinitialise, and put WS2 in
title bar. If you do not get a new copy of the INSTALL script, it
will not unpack the WS2 update files.
The database software has not changed. You should be using these
updates in conjunction with release 4_3 of the acedb software.
Reminder: there are now two versions of the C.elegans database. The
WS2 update series contains everything, whereas the WG2 update series
contains all data except sequences and directly related material
(proteins, motifs etc.), for those with limited resources.
The additions since the last release are:
for both types of update
- a physical map update with a few changes (mid Feb)
- accumulated genetic data and corrections
- from CGC : bibliography, wbg subscribers and strains (February)
- from Leon Avery : wbg14.5 with connections to genes etc.
and for just the complete database including sequences (WS2.4-16)
Data fom St Louis and Sanger Sequence databases taken in mid-Feb:
- There are now 2020 (1859 before) cosmids totalling 60615799
(55996632 before) bases.
- EMBL49 Sequence, dna and full embl text descriptions
- We have tried to include all the missing Peptide sequences, so you
do not see dashes in the blixem (multiple alignment) display.
The total database sizes after adding these updates are around 390MB
for the WS2 database and around 60MB for the WG2 database.
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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