WormBase release WS97 now online
"Wormbase" <[email protected]> Sat, 8 Mar 2003 03:26:33 -0500
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200303080826.h288QXk28159__19847.7775244557$1047112440@brie3.cshl.org> |
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 acedb WS97, Wormpep97 and Wormrna97 Fri Mar 7 2003
======================================================================
This directory includes:
i) database.WS97.*.tar.gz - compressed data for new release
ii) models.wrm.WS97 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS97-WS96.dbcomp - log file reporting difference from last release
v) wormpep97.tar.gz - full Wormpep distribution corresponding to WS97
vi) wormrna97.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS97.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 WS97
------------------------------------
brigdb : 2003-02-21 - updated
camace : 2003-02-25 - updated
citace : 2003-02-23 - updated
cshace : 2003-01-26
genace : 2003-03-05 - updated
stlace : 2003-02-24 - updated
Genome sequence composition:
----------------------------
WS97 WS96 change
----------------------------------------------
a 32364259 32364259 +0
c 17778485 17778485 +0
g 17755881 17755881 +0
t 32365361 32365361 +0
n 95 95 +0
- 0 0 +0
Total 100264081 100264081 +0
Wormpep data set:
----------------------------
There are 19542 CDS in autoace, 21437 when counting 1891 alternate splice forms.
The 21437 sequences contain 9,458,170 base pairs in total.
Modified entries 56
Deleted entries 10
New entries 24
Reappeared entries 3
Net change +17
Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed 3758 (17.5%)
Partially_confirmed 8875 (41.4%)
Predicted 8804 (41.1%)
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 2235 (10.4%)
TrEMBL accessions 18549 (86.5%)
TrEMBLnew accessions 641 (3.0%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 21425 (99.9%)
Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection 4204
GeneModel correction progress WS96 -> WS97
-----------------------------------------
Confirmed introns not is a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 619 | -1047 |
St Louis | 160 | 2 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 0 | -24 |
St Louis | 0 | -24 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
For more info mail [email protected]
-===================================================================================-
New Data:
---------
New ?Feature class to accomodate any feature to be mapped back
to the genome sequence (e.g. trans-splice leader, poly-A signal,
etc). Currently, 13,900 splice leader acceptor sites have been
added.
Local repeats have been moved in the models to the Feature_data
class. This does not affect anything in terms of data display
or GFF dumps.
The 'hybrid' gene set of C.briggsae predictions has been added
to WormBase. Orthologue pairs between C.elegans and C.briggsae
are annotated (Todd Harris analysis for WS77-cb25).
The briggsae data is available in GFF format (file cb25.agp8.gff.tar.gz
on the FTP site with the rest of the cb25.agp8 data). For more
information mail <[email protected]>.
New Fixes:
----------
RepeatMasker anlaysis has been extended to the whole of the genome
(i.e. includes WashU section).
Author class has been cleared up from WS96 meeting abstract parsing
problems.
Many TREMBLNEW SWALL accessions have been subsumed into the full release
of TREMBL 73.
Known Problems:
--------------
The additional RepeatMasker repeat families are too permisive, many
of them overlap with valid coding segments (i.e. they match multiple
gene families). These will be addressed over the coming weeks.
Changes to the repeat mappings have not been followed through to the
consistency checking scripts. The CDS overlapping repeat counts (see above)
are therefore incorrect and do not reflect the true situation.
Features have been assigned in an automated fashion. Currently, the
data set is redundant in terms of mapped trans-splice acceptors wherein
one feature has been assigned for each transcript. The process of adding
new features is an ongoing one and more will appear in future WormBase
releases.
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
Switch WormBase's view of the human proteome from Ensembl to the IPI
(see http://www.ebi.ac.uk/IPI/).
Change to models to handle GO codes, and curator_confirmed evidence.
Indexing the Also_known_as class to simplify the Author/Person 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.
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