From WormBaseWiki
New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb 8 15:28:27 GMT 2007
WS171 was built by Anthony
======================================================================
This directory includes:
i) database.WS171.*.tar.gz - compressed data for new release
ii) models.wrm.WS171 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS171-WS170.dbcomp - log file reporting difference from last release
v) wormpep171.tar.gz - full Wormpep distribution corresponding to WS171
vi) wormrna171.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS171.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS171.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS171.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS171.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS171.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.WS171.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS171.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS171.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:
----------------------------
WS171 WS170 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 23967)
------------------------------------------
Molecular_info 22274 (92.9%)
Concise_description 4401 (18.4%)
Reference 6731 (28.1%)
CGC_approved Gene name 8945 (37.3%)
RNAi_result 19843 (82.8%)
Microarray_results 19135 (79.8%)
SAGE_transcript 20061 (83.7%)
Wormpep data set:
----------------------------
There are 20085 CDS in autoace, 23226 when counting 3141 alternate splice forms.
The 23226 sequences contain 10,187,058 base pairs in total.
Modified entries 6
Deleted entries 4
New entries 3
Reappeared entries 3
Net change +2
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 7825 (33.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10745 (46.3%) Some, but not all exon bases are covered by transcript evidence
Predicted 4656 (20.0%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3489 (15.0%)
UniProtKB/TrEMBL accessions 19365 (83.4%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22854 (98.4%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7303
GeneModel correction progress WS170 -> WS171
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 15 | 0 |
St Louis | 13 | 3 |
+---------+--------+
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@sanger.ac.uk
-===================================================================================-
New Data:
---------
C.remanei orthologs assignments are now made using the WashU preliminary gene set.
Syntenic alignments of the genome sequence are still included in the compara download.
Genome sequence updates:
-----------------------
none
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
-------------------------------------
Model Changes:
------------------------------------
none
-===================================================================================-
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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