From WormBaseWiki
New release of WormBase WS160, Wormpep160 and Wormrna160 Thu Jun 15 16:29:46 BST 2006
WS160 was built by Ant and Michael
======================================================================
This directory includes:
i) database.WS160.*.tar.gz - compressed data for new release
ii) models.wrm.WS160 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS160-WS159.dbcomp - log file reporting difference from last release
v) wormpep160.tar.gz - full Wormpep distribution corresponding to WS160
vi) wormrna160.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS160.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS160.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS160.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS160.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS160.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.WS160.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS160.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS160.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
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http://wwwdev.sanger.ac.uk/Projects/C_elegans/WORMBASE
Genome sequence composition:
----------------------------
WS160 WS159 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 23757)
------------------------------------------
Molecular_info 22014 (92.7%)
Concise_description 4180 (17.6%)
Reference 5879 (24.7%)
CGC_approved Gene name 8801 (37%)
RNAi_result 19798 (83.3%)
Microarray_results 19126 (80.5%)
SAGE_transcript 18174 (76.5%)
Wormpep data set:
----------------------------
There are 20063 CDS in autoace, 23144 when counting 3081 alternate splice forms.
The 23144 sequences contain 10,164,788 base pairs in total.
Modified entries 38
Deleted entries 47
New entries 18
Reappeared entries 3
Net change -26
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 6712 (29.0%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11424 (49.4%) Some, but not all exon bases are covered by transcript evidence
Predicted 5008 (21.6%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3227 (13.9%)
UniProtKB/TrEMBL accessions 19623 (84.8%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22850 (98.7%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7114
GeneModel correction progress WS159 -> WS160
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 17 | -5 |
St Louis | 5 | -1 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 63 | - |
St Louis | 121 | - |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
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For more info mail worm@sanger.ac.uk
-===================================================================================-
New Data:
---------
There are ~18,000 new predicted interactions taken from "Zhong and Sternberg Science:Vol.311. pp.1481-1484"
~1300 new mos insertion alleles from the nemeGENTAG consortium
New Fixes:
----------
Known Problems:
--------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
New data models have been devised and agreed to allow the incorporation of Mass Spec protein analysis data to be included in WormBase.
We have data from several researchers, some of which will be inlcuded in a forthcoming release of the database.
Model Changes:
------------------------------------
Changes to Interaction and Interaction_type to allow inclusion of predicted interaction 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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