From WormBaseWiki
Release Notes
New release of WormBase WS178, Wormpep178 and Wormrna178 Wed Jul 4 12:56:45 BST 2007
WS178 was built by Gary Williams
======================================================================
This directory includes:
i) database.WS178.*.tar.gz - compressed data for new release
ii) models.wrm.WS178 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS178-WS177.dbcomp - log file reporting difference from last release
v) wormpep178.tar.gz - full Wormpep distribution corresponding to WS178
vi) wormrna178.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS178.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS178.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS178.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS178.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS178.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.WS178.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS178.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS178.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:
----------------------------
WS178 WS177 change
----------------------------------------------
a 32365888 32365888 +0
c 17779856 17779856 +0
g 17756017 17756017 +0
t 32365689 32365689 +0
n 0 0 +0
- 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 24134)
------------------------------------------
Molecular_info 22424 (92.9%)
Concise_description 4774 (19.8%)
Reference 7202 (29.8%)
CGC_approved Gene name 9318 (38.6%)
RNAi_result 19879 (82.4%)
Microarray_results 19570 (81.1%)
SAGE_transcript 18641 (77.2%)
Wormpep data set:
----------------------------
There are 20148 CDS in autoace, 23459 when counting 3311 alternate splice forms.
The 23459 sequences contain 10,307,638 base pairs in total.
Modified entries 60
Deleted entries 0
New entries 47
Reappeared entries 0
Net change +47
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 8084 (34.5%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10720 (45.7%) Some, but not all exon bases are covered by transcript evidence
Predicted 4655 (19.8%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3543 (15.1%)
UniProtKB/TrEMBL accessions 19490 (83.1%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 23033 (98.2%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7680
GeneModel correction progress WS177 -> WS178
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 68 | -11 |
St Louis | 156 | -29 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 6 | 0 |
St Louis | 6 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_V sequence Z72508
CHROMOSOME_X sequence Z67755
There are no gaps remaining in the genome sequence
---------------
For more info mail worm@sanger.ac.uk
-===================================================================================-
New Data:
---------
Swissprot has been updated to release 53.1
Trembl has been updated to release 36.1
Genome sequence updates:
-----------------------
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Curation of Caenorhabditis gene nomenclature and of the C. elegans
genetic map became part of WormBase. Previously, for the period June
1992 - May 2007, gene names and nomenclature were curated by Dr
Jonathan Hodgkin, as a subcontract of the Caenorhabditis Genetics
Center. Dr Hodgkin will continue to act for WormBase, as curator for
gene nomenclature and the genetic map. Gene naming and genetic map
enquiries should be directed to genenames@wormbase.org or
jonathan.hodgkin@bioch.ox.ac.uk.
All gene classes which were assigned to the CGC laboratory have been
moved to the newly created GNW (Gene Names at WormBase) laboratory.
Proposed Changes / Forthcoming Data:
-------------------------------------
Model Changes:
------------------------------------
Fixed WS177 error in Phenotype_info hash where Treatment, Temperature
and Genotype were incorrectly linking to non-existant classes
-===================================================================================-
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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