From WormBaseWiki
New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007
WS175 was built by [Anthony]
======================================================================
This directory includes:
i) database.WS175.*.tar.gz - compressed data for new release
ii) models.wrm.WS175 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS175-WS174.dbcomp - log file reporting difference from last release
v) wormpep175.tar.gz - full Wormpep distribution corresponding to WS175
vi) wormrna175.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS175.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS175.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS175.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS175.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS175.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.WS175.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS175.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS175.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:
----------------------------
WS175 WS174 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 24085)
------------------------------------------
Molecular_info 22393 (93%)
Concise_description 4579 (19%)
Reference 7004 (29.1%)
CGC_approved Gene name 9177 (38.1%)
RNAi_result 19871 (82.5%)
Microarray_results 19149 (79.5%)
SAGE_transcript 20043 (83.2%)
Wormpep data set:
----------------------------
There are 20115 CDS in autoace, 23273 when counting 3158 alternate splice forms.
The 23273 sequences contain 10,219,495 base pairs in total.
Modified entries 42
Deleted entries 8
New entries 21
Reappeared entries 2
Net change +15
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 7866 (33.8%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10792 (46.4%) Some, but not all exon bases are covered by transcript evidence
Predicted 4615 (19.8%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3496 (15.0%)
UniProtKB/TrEMBL accessions 19225 (82.6%)
GeneModel correction progress WS174 -> WS175
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 173 | -13 |
St Louis | 212 | -3 |
+---------+--------+
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
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For more info mail worm@sanger.ac.uk
-===================================================================================-
New Data:
---------
Database cross references to miRBase have been added to 131 genes.
Genome sequence updates:
-----------------------
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
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Model Changes:
------------------------------------
Added tags to ?Person and ?Paper to enable recording of negative connections ie Mr X did NOT contribue to this paper.
Added Map_evidence to ?Transgene so that the paper that mapping data is taken from can be attributed
Added a tags to ?Expr_pattern and  ?Expression_cluster to handle Localizome data
Changes in the ?Interaction model as proposed by Andrei. Added #Interactor_info and #Interaction_info
Directed_Y1H in YH 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.
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