WS210
From WormBaseWiki
Jump to navigationJump to searchNew release of WormBase WS210, Wormpep210 and Wormrna210 Tue Dec 22 12:35:31 GMT 2009
WS210 was built by Gary Williams
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This directory includes:
i) database.WS210.*.tar.gz - compressed data for new release
ii) models.wrm.WS210 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS210-WS209.dbcomp - log file reporting difference from last release
v) wormpep210.tar.gz - full Wormpep distribution corresponding to WS210
vi) wormrna210.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS210.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS210.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS210.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS210.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS210.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.WS210.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS210.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS210.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:
----------------------------
WS210 WS209 change
----------------------------------------------
a 32367418 32367418 +0
c 17780763 17780763 +0
g 17756943 17756943 +0
t 32367086 32367086 +0
n 0 0 +0
- 0 0 +0
Total 100272210 100272210 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 40052)
------------------------------------------
Molecular_info 38350 (95.8%)
Concise_description 5615 (14%)
Reference 13714 (34.2%)
WormBase_approved Gene name 25858 (64.6%)
RNAi_result 24280 (60.6%)
Microarray_results 21063 (52.6%)
SAGE_transcript 19069 (47.6%)
Wormpep data set:
----------------------------
There are 20254 CDS in autoace, 24273 when counting 4019 alternate splice forms.
The 24273 sequences contain 10,732,870 base pairs in total.
Modified entries 48
Deleted entries 28
New entries 65
Reappeared entries 2
Net change +39
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 9922 (40.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11599 (47.8%) Some, but not all exon bases are covered by transcript evidence
Predicted 2752 (11.3%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions 24137 (99.4%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 24137 (99.4%)
Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name 24204
GeneModel correction progress WS209 -> WS210
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 0 | 0 |
St Louis | 0 | 0 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 0 | 0 |
St Louis | 0 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail help@wormbase.org
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New Data:
---------
Blast databases updated:
brigpep210
ipi_human_11_06
gadfly36
remapep210
wormpep210
yeast38
This release includes 151 Feature objects marking the positions of
probable genome sequence errors.
This data is derived from analyses of the RNAseq data from LaDeana
Hillier and Bob Waterston:
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.
<http://www.ncbi.nlm.nih.gov/pubmed/19181841?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1>
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH.
Genome Res. 2009 Apr;19(4):657-66. Epub 2009 Jan 30.PMID: 19181841
It is expected that these probable genome sequence error positions wil be examined and corrected soon.
Genome sequence updates:
-----------------------
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
-------------------------------------
added Feature to Feature connection
Model Changes:
------------------------------------
added Assistant professor to #Role
-===================================================================================-
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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