WS207

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Release Notes

New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009


WS207 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS207.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS207           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS207-WS206.dbcomp         -   log file reporting difference from last release
v)   wormpep207.tar.gz          -   full Wormpep distribution corresponding to WS207
vi)   wormrna207.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS207.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS207.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS207.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS207.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS207.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.WS207.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS207.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS207.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:
----------------------------

       	WS207       	WS206      	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 39985)
------------------------------------------
Molecular_info              38279 (95.7%)
Concise_description          4925 (12.3%)
Reference                   13643 (34.1%)
WormBase_approved Gene name 25839 (64.6%)
RNAi_result                 22830 (57.1%)
Microarray_results          21055 (52.7%)
SAGE_transcript             19046 (47.6%)




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

There are 20231 CDS in autoace, 24185 when counting 3954 alternate splice forms.

The 24185 sequences contain 10,689,789 base pairs in total.

Modified entries      146
Deleted entries       25
New entries           67
Reappeared entries    3

Net change  +45
The differnce between the total CDS's of this (24185) and the last build (24143) does not equal the net change 45
Please investigate! ! 




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9819 (40.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11573 (47.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2793 (11.5%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24045 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24045 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24181


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:
---------
Duplicon region features from paper WBPaper00034747
http://www.wormbase.org/db/misc/paper?name=WBPaper00034747;class=Paper
WBsf038821 - WBsf042304

HTZ-1 binding site regions added WBPaper00032180
http://www.wormbase.org/db/misc/paper?name=WBPaper00032180;class=Paper
WBsf042314 - WBsf047477

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


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

Longtext EST/mRNA patched
  70,000 Sequence entries were missing their EMBL/GENBANK accession info inm 
  previous releases.


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


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

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


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


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


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 _____________

Patches

Protein

Some proteins have additional zombie proteins in their blast homology data. A patch to fix that is at ftp://ftp.sanger.ac.uk/pub2/wormbase/WS207/acedb/protein_patch.ace