ACEDB data updates for C.elegans

Richard Durbin rd at mrc-lmb.cam.ac.uk
Sat Sep 21 23:12:38 EST 1996


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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 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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