IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

ACEDB data release WS8 for C.elegans

Richard Durbin rd at sanger.ac.uk
Thu Nov 25 05:51:41 EST 1999


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 at sanger.ac.uk.

New ACEDB data release WS8 for C. elegans 
=========================================

This data release contains the current state of the genomic sequence,
including all finished data plus all the large unfinished fragments as
of a few weeks ago, totalling 96,893,008 true bases.  It also contains
the 1999 genetic map, and much other updated information.

We apologise for the delay since the previous release.  An
intermediary version (WS7) was made, but it was missing a significant
amount of data present in WS6, so was not formally announced.

Like the last few releases (WS5 onwards), this release is made as a
set of compressed database files (database.WS8.4-0.tar.Z,
database.WS8.4-1.tar.Z etc. up to 4-8), which the INSTALL script will
unpack into a working database - there is no need to "Add updates"
from inside acedb as previously.

You will need 2.5 GB of disk space to install.  Once installation
is finished you can remove the database.*.tar.Z files, leaving around
1.8 GB for the database plus program etc..

You MUST have a copy of the INSTALL script from September 1999 or
later.

You should be using these updates in conjunction with release 4_7 of
the acedb software (4_7l released summer 1999).  If you have a working
acedb version from since then, you do not need a new copy of the
program (the bin.<operating system>.* file).  If you are installing
into a new directory you will need an appropriate binary from the
.../acedb/ace4/ directory.

There is no WG8 database, containing the genetic data without the
sequence data.

Ancillary files
===============

Current sequences of each chromosome and accompanying feature tables
corresponding to this release are available in
ftp://ftp.sanger.ac.uk/pub/acedb/celegans/CHROMOSOMES.WS8/

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 in the USA, in repository/acedb
  ftp.sanger.ac.uk in England, in pub/acedb
  lirmm.lirmm.fr in France, in directory genome/acedb

In each case, log in as user "anonymous" and give an email address
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				# binary transfer mode - IMPORTANT
dir				# display files in this directory
get README
get NOTES
get INSTALL			# always get this
cd ace4				# change to ace4 directory
get bin.solaris._5_6.4_7l.tar.Z	# get program
cd ../celegans			# change to worm data directory
mget database.WS8.*		# get all WS5 database files
quit

--------------------------------

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
"csh INSTALL".

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 should be sent to the appropriate person on the contact list
at http://wormsrv1.sanger.ac.uk/cgi-bin/ace/feedback/.

-------------------- end of message --------------------
---





More information about the Acedb mailing list

Send comments to us at archive@iubioarchive.bio.net