WormBase release WS167 now online
"Todd Harris" <[email protected]> Sat, 2 Dec 2006 08:40:17 -0500
| Newsgroups | gmane.science.biology.wormbase.announce,gmane.science.biology.wormbase.general |
|---|---|
| Message-ID | <[email protected]> |
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
roughly every three 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/
or
ftp://ftp.wormbase.org/pub/wormbase/acedb/current_release
Additional information on the release, including any necessary patches or bug
fixes can be found on the WormBaseWiki:
http://www.wormbase.org/wiki/index.php/WSWS167
New release of WormBase WS167, Wormpep167 and Wormrna167 Thu Nov 9 11:42:25 GMT 2006
WS167 was built by [Michael]
======================================================================
This directory includes:
i) database.WS167.*.tar.gz - compressed data for new release
ii) models.wrm.WS167 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS167-WS166.dbcomp - log file reporting difference from last release
v) wormpep167.tar.gz - full Wormpep distribution corresponding to WS167
vi) wormrna167.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS167.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS167.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS167.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS167.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS167.gz - for each C. elegans WormPep protein, lists Best blastp match to
human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.
xii) best_blastp_hits_brigprot.WS167.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS167.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS167.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_notes
Genome sequence composition:
----------------------------
WS167 WS166 change
----------------------------------------------
a 32365888 32365888 +0
c 17779857 17779857 +0
g 17756012 17756012 +0
t 32365687 32365687 +0
n 0 0 +0
Total 100267444 100267444 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 23888)
------------------------------------------
Molecular_info 22174 (92.8%)
Concise_description 4149 (17.4%)
Reference 6547 (27.4%)
CGC_approved Gene name 8894 (37.2%)
RNAi_result 19831 (83%)
Microarray_results 19135 (80.1%)
SAGE_transcript 19725 (82.6%)
Wormpep data set:
----------------------------
There are 20089 CDS in autoace, 23222 when counting 3133 alternate splice forms.
The 23222 sequences contain 10,197,759 base pairs in total.
Modified entries 32
Deleted entries 10
New entries 24
Reappeared entries 1
Net change +15
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 7820 (33.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10751 (46.3%) Some, but not all exon bases are covered by transcript evidence
Predicted 4651 (20.0%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3270 (14.1%)
UniProtKB/TrEMBL accessions 19488 (83.9%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22758 (98.0%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7248
GeneModel correction progress WS166 -> WS167
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 14 | 0 |
St Louis | 10 | 0 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 6 | 0 |
St Louis | 6 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
Blast databases updated:
ipi_human (version 10_23)
gadfly (version 13)
yeast (version 20)
Two sets of Mass Spectrometry peptides were added from the papers
Wietsch N. et al. J. Proteome Res., 5(9), pp 2448-2456,2006
and
Husson J. et al. Biochemical and Biophysical Research Communications, 335(1),pp 76-86 2005
totalling 193 peptides
Genome sequence updates:
-----------------------
C.briggsae genomic sequence updated to cb3 assembly
New Fixes:
----------
Known Problems:
---------------
C.briggsae SNP substitution tag format is different to C.elegans (will be fixed in WS168)
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
-------------------------------------
Model Changes:
------------------------------------
MovieURL Text Added to ?Expr_pattern for wen to link to movie URLs
-===================================================================================-
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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