WS196

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New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008


WS196 was built by Mary Ann and Anthony
======================================================================

This directory includes:
i)   database.WS196.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS196           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS196-WS195.dbcomp         -   log file reporting difference from last release
v)   wormpep196.tar.gz          -   full Wormpep distribution corresponding to WS196
vi)   wormrna196.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS196.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS196.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS196.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS196.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS196.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.WS196.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS196.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS196.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:
----------------------------

       	WS196       	WS195      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779889	17779889	  +0
g    	17756041	17756041	  +0
t    	32365753	32365753	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267633	100267633	  +0


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


Gene data set (Live C.elegans genes 29872)
------------------------------------------
Molecular_info              28155 (94.3%)
Concise_description         5447 (18.2%)
Reference                   13254 (44.4%)
WormBase_approved Gene name 15636 (52.3%)
RNAi_result                 20799 (69.6%)
Microarray_results          20438 (68.4%)
SAGE_transcript             18838 (63.1%)




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

There are 20191 CDS in autoace, 23902 when counting 3711 alternate splice forms.

The 23902 sequences contain 10,518,004 base pairs in total.

Modified entries      66
Deleted entries       25
New entries           21
Reappeared entries    0

Net change  -4



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8517 (35.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10985 (46.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4400 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23768 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23772 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13967


GeneModel correction progress WS195 -> WS196
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     40  |    13  |
St Louis 	|    118  |    15  |
		+---------+--------+


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
---------------
For more info mail help@wormbase.org
-===================================================================================-



New Data:
---------
This release includes the C. brenneri genome for the first time.  Orthologies to the other species in WormBase have been determined and Gene names transferred from C. elegans where appropriate.

There has been some manual correction of the C. briggsae nGASP gene predictions.

Precalculated protein alignments are now made for each main WormBase species.
This is available on the Sanger FTP site ftp.sanger.ac.uk/pub2/wormbase/live_release/wormpep_clw.sql.bz2 . For info contact WormBase.

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


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


Known Problems:
---------------
Due to the amounts of data and time pressures to get C. brenneri in this release we didn't have time to load all of the blast hits for every species.
They are still available in the GFF files and so visible in the genome browser but not via querying the acedb database. 


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

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



Model Changes:
------------------------------------
added Person to #Affiliation


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


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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