From WormBaseWiki
Release Notes
New release of WormBase WS173, Wormpep173 and Wormrna173 Fri Mar 23 18:22:22 GMT 2007
WS173 was built by Michael Han
======================================================================
This directory includes:
i) database.WS173.*.tar.gz - compressed data for new release
ii) models.wrm.WS173 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS173-WS172.dbcomp - log file reporting difference from last release
v) wormpep173.tar.gz - full Wormpep distribution corresponding to WS173
vi) wormrna173.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS173.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS173.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS173.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS173.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS173.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.WS173.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS173.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS173.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:
----------------------------
WS173 WS172 change
----------------------------------------------
a 32365889 32365889 +0
c 17779856 17779856 +0
g 17756016 17756016 +0
t 32365689 32365689 +0
n 0 0 +0
Total 100267450 100267450 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 24019)
------------------------------------------
Molecular_info 22327 (93%)
Concise_description 4474 (18.6%)
Reference 6939 (28.9%)
CGC_approved Gene name 9084 (37.8%)
RNAi_result 19856 (82.7%)
Microarray_results 19143 (79.7%)
SAGE_transcript 20048 (83.5%)
there are 20106 CDS in autoace, 23258 when counting (3152) alternate splice_forms
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 7805 (33.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10840 (46.6%) Some, but not all exon bases are covered by transcript evidence
Predicted 4613 (19.8%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3504 (15.1%)
UniProtKB/TrEMBL accessions 19421 (83.5%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22898 (98.5%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7443
GeneModel correction progress WS172 -> WS173
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 184 | -1 |
St Louis | 215 | 1 |
+---------+--------+
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 worm@sanger.ac.uk
-===================================================================================-
New Data:
---------
* added Nemagenetag dbinfo for crossreferencing with the Nemagene website
* Deletion_validation data added to variations to show additional experimental evidence
Genome sequence updates:
-----------------------
* change of ownership for some genomic clones between WashU and Sanger
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
-------------------------------------
Model Changes:
------------------------------------
* made Reference UNIQUE in RNAi class
-===================================================================================-
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.
