WS187

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Release Notes

New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008


WS187 was built by Gary Williams (gw3@sanger.ac.uk)
======================================================================

This directory includes:
i)   database.WS187.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS187           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS187-WS186.dbcomp         -   log file reporting difference from last release
v)   wormpep187.tar.gz          -   full Wormpep distribution corresponding to WS187
vi)   wormrna187.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS187.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS187.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS187.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS187.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS187.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.WS187.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS187.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS187.gz   - Mappings between PCR products and overlapping Genes


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



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

       	WS187       	WS186      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779886	17779886	  +0
g    	17756037	17756037	  +0
t    	32365750	32365750	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267623	100267623	  +0


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


Gene data set (Live C.elegans genes 29647)
------------------------------------------
Molecular_info              27947 (94.3%)
Concise_description         5147 (17.4%)
Reference                   7586 (25.6%)
WormBase_approved Gene name 15172 (51.2%)
RNAi_result                 20736 (69.9%)
Microarray_results          19963 (67.3%)
SAGE_transcript             18732 (63.2%)




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

There are 20170 CDS in autoace, 23662 when counting 3492 alternate splice forms.

The 23662 sequences contain  base pairs in total.

Modified entries      50
Deleted entries       18
New entries           35
Reappeared entries    0

Net change  +17



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8337 (35.2%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10964 (46.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4361 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3678 (15.5%)
UniProtKB/TrEMBL accessions     19707 (83.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23385 (98.8%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13522


GeneModel correction progress WS186 -> WS187
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    127  |     3  |
St Louis 	|    404  |   -68  |
		+---------+--------+


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:
---------

Blast database versions:
ipi_human_01_08.pep
yeast28.pep

TreeFam IDs are now imported for multiple isoforms of a gene.


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


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


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


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

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


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

added Variation_evidence to Evidence hash


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


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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