WormBase release WS174 now online
"Todd Harris" <[email protected]> Sun, 6 May 2007 12:53:52 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200705061653.l46GrqR2000313__33674.0288454623$1178470794$gmane$org@brie6.cshl.edu> |
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. 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
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/WSWS174
New release of WormBase WS174, Wormpep174 and Wormrna174 Fri Apr 13 11:04:50 BST 2007
WS174 was built by Gary Williams
======================================================================
This directory includes:
i) database.WS174.*.tar.gz - compressed data for new release
ii) models.wrm.WS174 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS174-WS173.dbcomp - log file reporting difference from last release
v) wormpep174.tar.gz - full Wormpep distribution corresponding to WS174
vi) wormrna174.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS174.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS174.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS174.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS174.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS174.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.WS174.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS174.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS174.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:
----------------------------
WS174 WS173 change
----------------------------------------------
a 32365889 32365889 +0
c 17779856 17779856 +0
g 17756016 17756016 +0
t 32365689 32365689 +0
n 0 0 +0
Total 100267450 100267450 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 24036)
------------------------------------------
Molecular_info 22345 (93%)
Concise_description 4524 (18.8%)
Reference 6981 (29%)
CGC_approved Gene name 9116 (37.9%)
RNAi_result 19859 (82.6%)
Microarray_results 19140 (79.6%)
SAGE_transcript 20044 (83.4%)
Wormpep data set:
----------------------------
There are 20101 CDS in autoace, 23258 when counting 3157 alternate splice forms.
The 23258 sequences contain 10,212,175 base pairs in total.
Modified entries 26
Deleted entries 8
New entries 6
Reappeared entries 2
Net change +0
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 7848 (33.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10802 (46.4%) Some, but not all exon bases are covered by transcript evidence
Predicted 4608 (19.8%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3512 (15.1%)
UniProtKB/TrEMBL accessions 19384 (83.3%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22869 (98.3%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7476
GeneModel correction progress WS173 -> WS174
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 186 | 2 |
St Louis | 215 | 0 |
+---------+--------+
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 [email protected]
-===================================================================================-
New Data:
---------
The following databases were updated for BLAST:
trembl release 35
swissprot release 52
yeast
Genome sequence updates:
-----------------------
None.
New Fixes:
----------
None.
Known Problems:
---------------
Other Changes:
--------------
Many Poly-A tails were masked in EST and mRNA sequences. New Poly-A
Site and Poly-A Signal sequence Features were defined based on the
alignment of these sequences to the genome:
- 3530 new (1931 site, 1599 signal sequence) Features were defined.
- 641 old Poly-A Features (490 site, 151 signal) with no supporting
Sequence evidence were removed (changed to Method="history").
Proposed Changes / Forthcoming Data:
-------------------------------------
We are working with the authors of this paper:
Ruby J et al. Cell. 2006 Dec 15;127(6):1193-207. "Large-scale
sequencing reveals 21U-RNAs and additional microRNAs and endogenous
siRNAs in C. elegans."
http://www.wormbase.org/db/misc/paper?name=WBPaper00028915;class=Paper
to refine and annotate circa 4500 new elegans RNA genes.
<A third class of nematode small RNAs, called 21U-RNAs, was
discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a
uridine 5''-monophosphate but are diverse in their remaining 20
nucleotides, and appear modified at their 3''-terminal
ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed
in two broad regions of chromosome IV-primarily between protein-coding
genes or within their introns. These loci share a large upstream motif
that enables accurate prediction of additional 21U-RNAs. The motif is
conserved in other nematodes, presumably because of its importance for
producing these diverse, autonomously expressed, small RNAs
(dasRNAs).>
Forthcoming model changes:
Added tags to ?Person and ?Paper to enable recording of negative
connections ie Mr X did NOT contribue to this paper.
Added Map_evidence to ?Transgene so that the paper that mapping data
is taken from can be attributed
Added a tags to ?Expr_pattern and ?Expression_cluster to handle
Localizome data Note: ?Interaction class update already committed
Model Changes:
------------------------------------
Added DB_info line to ?Gene
Replaced ?Y2H with a more generic ?YH class which contains Y2H and Y1H
data.
Added Anatomy_function class to allow the connection between
?Anatomy_term, ?Phenotype (proxy of biological function), and ?Gene
and still give some information about the experiment itself. Name
shall be "WBbtf0001"
-===================================================================================-
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 _____________