WS203

From WormBaseWiki
Jump to: navigation, search

Release letter

New release of WormBase WS203, Wormpep203 and Wormrna203 Thu May 28 13:24:17 BST 2009


WS203 was built by gw3
======================================================================

This directory includes:
i)   database.WS203.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS203           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS203-WS202.dbcomp         -   log file reporting difference from last release
v)   wormpep203.tar.gz          -   full Wormpep distribution corresponding to WS203
vi)   wormrna203.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS203.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS203.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS203.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS203.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS203.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.WS203.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS203.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS203.gz   - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_Schedule



Genome sequence composition:
----------------------------

       	WS203       	WS202      	change
----------------------------------------------
a    	32367418	32367418	  +0
c    	17780763	17780763	  +0
g    	17756943	17756943	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272210	100272210	  +0


Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.


Gene data set (Live C.elegans genes 39896)
------------------------------------------
Molecular_info              38186 (95.7%)
Concise_description         5468 (13.7%)
Reference                   13432 (33.7%)
WormBase_approved Gene name 25783 (64.6%)
RNAi_result                 22783 (57.1%)
Microarray_results          21040 (52.7%)
SAGE_transcript             18934 (47.5%)




Wormpep data set:
----------------------------

There are 20178 CDS in autoace, 24032 when counting 3853 alternate splice forms.

The 24032 sequences contain 10,623,166 base pairs in total.

Modified entries      59
Deleted entries       17
New entries           20
Reappeared entries    0

Net change  +3



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9698 (40.4%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11543 (48.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2791 (11.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  22999 (95.7%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22999 (95.7%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24123


Synchronisation with GenBank / EMBL:
------------------------------------

No synchronisation issues


There are no gaps remaining in the genome sequence
---------------
For more info mail help@wormbase.org
-===================================================================================-



New Data:
---------

C. elegans 454 sequence data for WASHU 
See the RNAseq_Mitreva_454_elegans Analysis object in WS203


Genome sequence updates:
-----------------------


New Fixes:
----------


Known Problems:
---------------


Other Changes:
--------------

Proposed Changes / Forthcoming Data:
-------------------------------------

WS204 model change:
Fixed Transposon white space issues.


Model Changes:
------------------------------------

?Feature
Defined_by_analysis ?Analysis  //ar2 eg for chip-seq/chip derived binding site.

?Gene
Paralog ?Gene XREF Paralog ?Species #Evidence  //mh6 for adding paralogs



?Analysis & ?Condition improvement driven by need to show modENCODE metadata

?Analysis
Sample ?Condition XREF Analysis     //placing under Description tag

?Condition
Analysis ?Analysis XREF Sample           //under SAGE_experiment tag
Tissue ?Anatomy_term   //replacing Cell_type tag


Changes to Transposon and Pseudogene class so that we can correctly represent non-functional transposons


-===================================================================================-


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.

____________  END _____________