WormBase release WS113 now online
"WormBase" <[email protected]> Sun, 9 Nov 2003 16:53:25 -0500
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200311092153.hA9LrPj31467__9608.15326911888$1068415446@brie6.cshl.org> |
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
roughly every 2 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.sanger.ac.uk/pub/wormbase/current_release/
New release of WormBase WS113, Wormpep113 and Wormrna113 031103
===============================================================
This directory includes:
i) database.WS113.*.tar.gz - compressed data for new release
ii) models.wrm.WS113 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS113-WS112.dbcomp - log file reporting difference from last release
v) wormpep113.tar.gz - full Wormpep distribution corresponding to WS113
vi) wormrna113.tar.gz - WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS113.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) yk2orf.WS113.gz - Latest set of ORF connections to each Yuji Kohara EST clone
ix) gene_interpolated_map_positions.WS113.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS113.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS113.gz - for each C. elegans WormPep protein, lists Best blastp match
to human, fly, yeast, briggsae, and SwissProt & Trembl proteins.
xii) best_blastp_hits_brigprot.WS113.gz - for each C. briggsae protein, lists Best blastp match to human,
fly, yeast, C. elegans, and SwissProt & Trembl proteins.
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS113
------------------------------------
brigdb : 2003-10-20 - updated
camace : 2003-10-22 - updated
citace : 2003-10-17 - updated
cshace : 2003-10-17 - updated
genace : 2003-10-21 - updated
stlace : 2003-10-20 - updated
Genome sequence composition:
----------------------------
WS113 WS112 change
----------------------------------------------
a 32368607 32367165 +1442
c 17780992 17780236 + 756
g 17758424 17757587 + 837
t 32369797 32368413 +1384
n 95 95 0
- 0 0 0
---------------------------------------------
Total 100277915 100273496 +4419
Incorporation of a new segment VB0395L to chromosome X. This unfolds a repeat
and adds a net gain of 4419 bp to the consensus sequence.
Wormpep data set:
----------------------------
There are 19935 CDS in autoace, 22220 when counting 2285 alternate splice forms.
The 22220 sequences contain 9,696,674 base pairs in total.
Modified entries 21
Deleted entries 3
New entries 8
Reappeared entries 0
Net change +5
Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed 4369 (19.7%)
Partially_confirmed 10953 (49.3%)
Predicted 6898 (31.0%)
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 2420 (10.9%)
TrEMBL accessions 18899 (85.1%)
TrEMBLnew accessions 883 (4.0%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22202 (99.9%)
Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection 4493
GeneModel correction progress WS112 -> WS113
-----------------------------------------
Confirmed introns not is a CDS gene model;
+----------+--------+
| Introns | Change |
+----------+--------+
Cambridge | 688 | 7 |
St Louis | 415 | -17 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+----------+--------+
| Families | Change |
+----------+--------+
Cambridge | 0 | 0 |
St Louis | 33 | 1 |
+----------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues with regard to DNA. A small number of CDS prediction
problems {C04A2|C04F5|C56E6|F53F4|T13C2}
There are no gaps remaining in the genome sequence
--------------------------------------------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
Re-analysis of TSL/Oligo cap Feature_data, (removal of false positives and incorporation of new data).
Transcripts are masked (a la repeatmasker) to remove TSL sequences, etc. This will be extended
to include polyA+ tails from mRNAs for the next release.
mos insertion alleles from Laurent Segalat
New Fixes:
----------
Corrected script which connects ?Microarray_results to genes/transcripts/loci.
Known Problems:
--------------
No BlastX/P data for the new segment VB0395L, (lag period for ensembl analysis).
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
BlastX/P data for the new segment VB0395L.
Re-analysis of small protein-coding genes (krb)
Removal of polyA+ tails from mRNA sequences prior to BLAT analysis.
Mechanism for removing transcripts from the BLAT analysis (e.g. all those ESTs which
map to the rRNA cluster).
-===================================================================================-
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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