WormBase release WS161 now online
"WormBase" <[email protected]> Mon, 31 Jul 2006 17:53:42 -0400
| 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/WSWS161
New release of WormBase WS161, Wormpep161 and Wormrna161 Mon Jul 10 14:48:41 BST 2006
WS161 was built by Mary Ann (and Anthony)
======================================================================
This directory includes:
i) database.WS161.*.tar.gz - compressed data for new release
ii) models.wrm.WS161 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS161-WS160.dbcomp - log file reporting difference from last release
v) wormpep161.tar.gz - full Wormpep distribution corresponding to WS161
vi) wormrna161.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS161.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS161.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS161.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS161.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS161.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.WS161.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS161.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS161.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
-------------------------
http://wwwdev.sanger.ac.uk/Projects/C_elegans/WORMBASE
Genome sequence composition:
----------------------------
WS161 WS160 change
----------------------------------------------
a 32365888 32365888 +0
c 17779855 17779855 +0
g 17756011 17756011 +0
t 32365687 32365687 +0
n 0 0 +0
Total 100267441 100267441 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 23756)
------------------------------------------
Molecular_info 22014 (92.7%)
Concise_description 4181 (17.6%)
Reference 6240 (26.3%)
CGC_approved Gene name 8822 (37.1%)
RNAi_result 19793 (83.3%)
Microarray_results 19117 (80.5%)
SAGE_transcript 18167 (76.5%)
Wormpep data set:
----------------------------
There are 20065 CDS in autoace, 23148 when counting 3083 alternate splice forms.
The 23148 sequences contain 10,165,614 base pairs in total.
Modified entries 18
Deleted entries 8
New entries 12
Reappeared entries 0
Net change +4
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 7724 (33.4%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10798 (46.6%) Some, but not all exon bases are covered by transcript evidence
Predicted 4626 (20.0%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3225 (13.9%)
UniProtKB/TrEMBL accessions 19125 (82.6%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22350 (96.6%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7135
GeneModel correction progress WS160 -> WS161
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 16 | -1 |
St Louis | 5 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
41500 new ESTs have been released to the public databases from the unpublished "Exelixis Caenorhabditis elegans
EST project". This has led to a large jump in the number of CDS structures that have a 'confirmed' status.
Nearly 2500 strains carrying transposon-tagged genes have been entered as part of the NemaGENTAG project.
The #Molecular_change has been populated in about 15,000 Variation objects, detailing the molecular change
produced by the Variation.
New Fixes:
----------
Known Problems:
--------------
Some Variation objects on chromosome X are missing Molecular_change data.
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
Model Changes:
------------------------------------
1) Added tags to track history of merges and splits in operons.
2) Tag for identifying nemaGENTAG variations.
-===================================================================================-
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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