From WormBaseWiki
New release of WormBase WS197, Wormpep197 and Wormrna197 Wed Nov 26 19:40:37 GMT 2008
WS197 was built by gw3
======================================================================
This directory includes:
i) database.WS197.*.tar.gz - compressed data for new release
ii) models.wrm.WS197 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS197-WS196.dbcomp - log file reporting difference from last release
v) wormpep197.tar.gz - full Wormpep distribution corresponding to WS197
vi) wormrna197.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS197.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS197.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS197.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS197.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS197.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.WS197.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS197.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS197.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:
----------------------------
WS197 WS196 change
----------------------------------------------
a 32367419 32365950 +1469
c 17780761 17779889 +872
g 17756942 17756041 +901
t 32367086 32365753 +1333
n 0 0 +0
- 0 0 +0
Total 100272208 100267633 +4575
Chromosomal Changes:
--------------------
Chromosome: III
10369319 10369318 0 -> 10369319 10369319 1
Chromosome: V
19683587 19683646 60 -> 19683587 19688220 4634
Gene data set (Live C.elegans genes 29869)
------------------------------------------
Molecular_info 28156 (94.3%)
Concise_description 5482 (18.4%)
Reference 13267 (44.4%)
WormBase_approved Gene name 15667 (52.5%)
RNAi_result 20796 (69.6%)
Microarray_results 20428 (68.4%)
SAGE_transcript 18839 (63.1%)
Wormpep data set:
----------------------------
There are 20191 CDS in autoace, 23938 when counting 3747 alternate splice forms.
The 23938 sequences contain 10,548,489 base pairs in total.
Modified entries 136
Deleted entries 41
New entries 76
Reappeared entries 0
Net change +35
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 8529 (35.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11001 (46.0%) Some, but not all exon bases are covered by transcript evidence
Predicted 4408 (18.4%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions 23809 (99.5%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 23810 (99.5%)
Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name 14003
GeneModel correction progress WS196 -> WS197
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 38 | -2 |
St Louis | 118 | 0 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 6 | 0 |
St Louis | 6 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_III sequence Z35641
CHROMOSOME_V sequence AL032637
CHROMOSOME_V sequence AL032637
There are no gaps remaining in the genome sequence
---------------
For more info mail [mailto:help@wormbase.org help@wormbase.org]
-===================================================================================-
New Data:
---------
These BLAST databases were updated:
gadfly release 26
ipi_human release 10_15
Genome sequence updates:
-----------------------
These was a 1 bp insertion in Chromosome III and a 4.6 Kb insertion in Chromosome V.
New Fixes:
----------
None.
Known Problems:
---------------
None.
Other Changes:
--------------
None.
Proposed Changes / Forthcoming Data:
-------------------------------------
None.
Model Changes:
------------------------------------
added Derived_from_matrix to the class ?Position_Matrix
-===================================================================================-
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 [http://www.acedb.org/ 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 _____________
