WS208

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New release of WormBase WS208, Wormpep208 and Wormrna208 Tue Oct 27 13:31:22 GMT 2009


WS208 was built by Anthony
======================================================================

This directory includes:
i)   database.WS208.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS208           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS208-WS207.dbcomp         -   log file reporting difference from last release
v)   wormpep208.tar.gz          -   full Wormpep distribution corresponding to WS208
vi)   wormrna208.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS208.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS208.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS208.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS208.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS208.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.WS208.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS208.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS208.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:
----------------------------

       	WS208       	WS207      	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 39999)
------------------------------------------
Molecular_info              38295 (95.7%)
Concise_description         5605 (14%)
Reference                   13653 (34.1%)
WormBase_approved Gene name 25843 (64.6%)
RNAi_result                 22833 (57.1%)
Microarray_results          21058 (52.6%)
SAGE_transcript             19056 (47.6%)




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

There are 20238 CDS in autoace, 24202 when counting 3964 alternate splice forms.

The 24202 sequences contain 10,693,111 base pairs in total.

Modified entries      13
Deleted entries       12
New entries           29
Reappeared entries    0

Net change  +17



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9843 (40.7%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11605 (48.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2754 (11.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24062 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24062 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24187

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:
---------
H.contortus included in orthology determination.

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


New Fixes:
----------
Some abherrant gene names have been removed.

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


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

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


Model Changes:
------------------------------------
added Title to ?Analysis


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


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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