WormBase release WS83 now online
"WormBase" <[email protected]> Mon, 5 Aug 2002 10:12:10 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <[email protected]> |
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
every two weeks.
The text of the AceDB release notes, which contains highlights of the
new data is attached. You can download the full AceDB files from:
ftp://ftp.wormbase.org/pub/wormbase/current_release/
New Release of WormBase WS83, Wormpep83 and Wormrna83 2/8/02
======================================================================
This directory includes:
i) database.WS83.*.tar.gz - compressed data for new release
ii) models.wrm.WS83 - the latest database schema (also in
above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per
chromosome)
iv) WS83-WS82.dbcomp - log file reporting difference from
last release
v) wormpep83.tar.gz - full Wormpep distribution
corresponding to WS83
vi) wormrna83.tar.gz - latest WormRNA release containing
non-coding RNA's in the genome
vii) confirmed_genes.WS83.gz - DNA sequences of all genes confirmed
by EST &/or cDNA
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS83
------------------------------------
brigdb : 2002-07-19 - updated
camace : 2002-07-23 - updated
citace : 2002-07-19 - updated
cshace : 2002-06-30
genace : 2002-07-22 - updated
stlace : 2002-07-19 - updated
Genome sequence composition:
----------------------------
WS83 WS82 change
----------------------------------------------
a 32344796 32341760 +3036
c 17767733 17763359 +4374
g 17745345 17743847 +1498
t 32346366 32340044 +6322
n 95 95 +0
- 62800 62800 +0
----------------------------------------------
Total 100267135 100251905 +15230
This is a net increase of 15,230 bp coming mainly from the incorporation
of the telomere IIR (clone name 2RSSE).
Remaining gaps:
---------------
For more info mail [email protected]
# Gaps are covered by a 950Kb SseI fragment
III 1005794 1028769 37 F AC087078.1 1 22976 +
III 1028770 1029769 38 N 1000
III 1029770 1075569 39 F AC084156.1 1 45800 +
# Gaps are covered by YAC clones in production at St Louis
X 1 2649 1 F AL031272.2 1 2649 +
X 2650 3649 2 N 1000
X 3650 14860 3 F AC087735.2 1 11211 +
X 177585 194657 6 F AC084160.2 1 17073 +
X 194658 225057 7 N 30400
X 225058 254821 8 F Z83097.1 1 29764 +
X 225058 254821 8 F Z83097.1 1 29764 +
X 254822 285221 9 N 30400
X 285222 299761 10 F AC024789.1 1 14540 +
Wormpep data set:
----------------------------
There are 19466 CDS in autoace, 20732 when counting 1266 alternate splice forms.
The 20732 sequences contain 9,156,670 base pairs in total.
Modified entries 71
Deleted entries 34
New entries 74
Reappeared entries 4
================================
Net change +44
GeneModel correction progress WS82 -> WS83
-----------------------------------------
Confirmed introns not is a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 1973 | -34 |
St Louis | 683 | -107 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 29 | 0 |
St Louis | 184 | -1 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_I sequence AC024866
CHROMOSOME_I sequence AC024866
CHROMOSOME_I sequence U88309
CHROMOSOME_I sequence AF106574
CHROMOSOME_II sequence AC084157
CHROMOSOME_II sequence AC087080
CHROMOSOME_II sequence AC084156
CHROMOSOME_III sequence U39851
CHROMOSOME_IV sequence U61957
CHROMOSOME_IV sequence U61957
CHROMOSOME_IV sequence U58755
CHROMOSOME_X sequence U40426
CHROMOSOME_X sequence U41542
CHROMOSOME_X sequence U53344
CHROMOSOME_X sequence U40945
----------------------------------------------------------------
New Data:
---------
C.briggsae sequence data is in WS83. The DNA is represented by the
GSC fosmids (accession.ver_no) and raw contigs cxxxxxxxxx.Contigx.
These are assembled into 'ultracontigs' using a AGP_fragment S_Child
SMap procedure. The 'ultracontigs' are named cb25.fpcxxxx and
cb25.NA_XXX. These 578 sequences have been submitted to EMBL.
A new UTR class is present in WS83 based on the initial mappings of
Lincoln Stein. Nomenclature is UTRxxxxxx and they are attached to the
Predicted_gene subclass via the Matching_UTR tag.
New sequence includes corrections from St Louis and the IIR telomeric
clone 2RSSE.
The wormpep history has been integrated into the database such that
prediction changes and name changes should be more transparent to the
user.
New Transgenes, strains, alleles, and loci (amongst others).
New Fixes:
----------
Known Problems:
--------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
Large number of gene model changes to come from Sanger.
Improvement of the UTR class.
Gene predictions for C.briggsae data.
Quick installation guide for UNIX/Linux systems
-----------------------------------------------
1. Create a new directory to contain your copy of WormBase,
e.g. /users/yourname/wormbase
2. Unpack and untar all of the database.*.tar.gz files into
this directory. You will need approximately 2-3 Gb of disk space.
3. Obtain and install a suitable acedb binary for your system
(available from www.acedb.org).
4. Use the acedb 'xace' program to open your database, e.g.
type 'xace /users/yourname/wormbase' at the command prompt.
5. See the acedb website for more information about acedb and
using xace.
____________ END _____________