WS200

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Release letter

New release of WormBase WS200, Wormpep200 and Wormrna200 Tue Feb 24 12:51:18 GMT 2009


WS200 was built by Anthony
======================================================================

This directory includes:
i)   database.WS200.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS200           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS200-WS199.dbcomp         -   log file reporting difference from last release
v)   wormpep200.tar.gz          -   full Wormpep distribution corresponding to WS200
vi)   wormrna200.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS200.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS200.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS200.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS200.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS200.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.WS200.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS200.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS200.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:
----------------------------

       	WS200       	WS199      	change
----------------------------------------------
a    	32367419	32367419	  +0
c    	17780761	17780761	  +0
g    	17756942	17756942	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272208	100272208	  +0


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


Gene data set (Live C.elegans genes 39868)
------------------------------------------
Molecular_info              35554 (89.2%)
Concise_description         5545 (13.9%)
Reference                   13406 (33.6%)
WormBase_approved Gene name 25733 (64.5%)
RNAi_result                 22045 (55.3%)
Microarray_results          20717 (52%)
SAGE_transcript             18841 (47.3%)




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

There are 20168 CDS in autoace, 23973 when counting 3805 alternate splice forms.

The 23973 sequences contain 10,580,574 base pairs in total.

Modified entries      28
Deleted entries       17
New entries           17
Reappeared entries    0

Net change  +0



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8704 (36.3%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11719 (48.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted              3550 (14.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23852 (99.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23852 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  21468


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:
---------
This archival release includes a new C. japonica assembly and associated set of gene predictions based on the methods determined by the nGASP project.

The C. brenneri gene set has been significantly improved through a manual curation effort.

Genome sequence updates:
-----------------------
None

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


Known Problems:
---------------
We have discovered a long standing problem with the parsing of the blat outputs where sequences from other species are aligned to a genome.  Only a small fraction of hits are affected but this does result in some odd alignments of ESTs to gaps in the contig based assemblies (which is what brought this to light).  The alignments of transcripts to the their genome of origin is NOT affected.

We are working to fix this asap but in the mean time if you are interested in any cross species alignments of transcript data in WormBase that look odd please double check them with the BLAT server provided at UCSC ( http://genome.ucsc.edu/cgi-bin/hgBlat )

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

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


Model Changes:
------------------------------------
None made

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


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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