WormBase release WS187 now online
Todd Harris <harris <at> cshl.edu>
2008-02-16 08:29:34 GMT
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
roughly every three weeks.
The text of the AceDB release notes, which contains highlights of the
new data is attached.
Additional information on the release, including any necessary patches or bug
fixes can be found on the WormBaseWiki:
http://www.wormbase.org/wiki/index.php/WSWS187
Downloads:
------------
You can download the full AceDB files from:
ftp://ftp.sanger.ac.uk/pub/wormbase/current_release/
or
ftp://ftp.wormbase.org/pub/wormbase/acedb/current_release
Running WormBase Locally:
---------------------------
If you would like to run WormBase on your own computer,
check out the WormBase Virtual Machine for this release:
ftp://ftp.wormbase.org/pub/wormbase/people/tharris/vmx/WS187
Documentation is available on the WormBase Wiki:
http://www.wormbase.org/wiki/index.php/Virtual_Machines
New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008
WS187 was built by Gary Williams
======================================================================
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 worm <at> sanger.ac.uk
-===================================================================================-
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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