https://wiki.wormbase.org/index.php?title=WS175&feed=atom&action=history
WS175 - Revision history
2024-03-28T15:49:40Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://wiki.wormbase.org/index.php?title=WS175&diff=13173&oldid=prev
Pdavis at 10:54, 21 December 2011
2011-12-21T10:54:33Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:54, 21 December 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l126" >Line 126:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> There are no gaps remaining in the genome sequence</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> There are no gaps remaining in the genome sequence</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> ---------------</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> ---------------</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> For more info mail <del class="diffchange diffchange-inline">worm</del>@<del class="diffchange diffchange-inline">sanger</del>.<del class="diffchange diffchange-inline">ac.uk</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> For more info mail <ins class="diffchange diffchange-inline">help</ins>@<ins class="diffchange diffchange-inline">wormbase</ins>.<ins class="diffchange diffchange-inline">org</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> -===================================================================================-</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> -===================================================================================-</div></td></tr>
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Pdavis
https://wiki.wormbase.org/index.php?title=WS175&diff=71&oldid=prev
Tharris: New page: <nowiki> New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 WS175 was built by [Anthony] ========================================================...
2007-09-23T21:32:28Z
<p>New page: <nowiki> New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 WS175 was built by [Anthony] ========================================================...</p>
<p><b>New page</b></p><div> <nowiki><br />
New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007<br />
<br />
<br />
WS175 was built by [Anthony]<br />
======================================================================<br />
<br />
This directory includes:<br />
i) database.WS175.*.tar.gz - compressed data for new release<br />
ii) models.wrm.WS175 - the latest database schema (also in above database files)<br />
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF &amp; AGP per chromosome)<br />
iv) WS175-WS174.dbcomp - log file reporting difference from last release<br />
v) wormpep175.tar.gz - full Wormpep distribution corresponding to WS175<br />
vi) wormrna175.tar.gz - latest WormRNA release containing non-coding RNA's in the genome<br />
vii) confirmed_genes.WS175.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA<br />
viii) cDNA2orf.WS175.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)<br />
ix) gene_interpolated_map_positions.WS175.gz - Interpolated map positions for each coding/RNA gene<br />
x) clone_interpolated_map_positions.WS175.gz - Interpolated map positions for each clone<br />
xi) best_blastp_hits.WS175.gz - for each C. elegans WormPep protein, lists Best blastp match to<br />
human, fly, yeast, C. briggsae, and SwissProt &amp; TrEMBL proteins.<br />
xii) best_blastp_hits_brigprot.WS175.gz - for each C. briggsae protein, lists Best blastp match to<br />
human, fly, yeast, C. elegans, and SwissProt &amp; TrEMBL proteins.<br />
xiii) geneIDs.WS175.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)<br />
xiv) PCR_product2gene.WS175.gz - Mappings between PCR products and overlapping Genes<br />
<br />
<br />
Release notes on the web:<br />
-------------------------<br />
http://www.wormbase.org/wiki/index.php/Release_notes<br />
<br />
<br />
<br />
Genome sequence composition:<br />
----------------------------<br />
<br />
WS175 WS174 change<br />
----------------------------------------------<br />
a 32365889 32365889 +0<br />
c 17779856 17779856 +0<br />
g 17756016 17756016 +0<br />
t 32365689 32365689 +0<br />
n 0 0 +0<br />
<br />
Total 100267450 100267450 +0<br />
<br />
<br />
Chromosomal Changes:<br />
--------------------<br />
There are no changes to the chromosome sequences in this release.<br />
<br />
<br />
Gene data set (Live C.elegans genes 24085)<br />
------------------------------------------<br />
Molecular_info 22393 (93%)<br />
Concise_description 4579 (19%)<br />
Reference 7004 (29.1%)<br />
CGC_approved Gene name 9177 (38.1%)<br />
RNAi_result 19871 (82.5%)<br />
Microarray_results 19149 (79.5%)<br />
SAGE_transcript 20043 (83.2%)<br />
<br />
<br />
<br />
<br />
Wormpep data set:<br />
----------------------------<br />
<br />
There are 20115 CDS in autoace, 23273 when counting 3158 alternate splice forms.<br />
<br />
The 23273 sequences contain 10,219,495 base pairs in total.<br />
<br />
Modified entries 42<br />
Deleted entries 8<br />
New entries 21<br />
Reappeared entries 2<br />
<br />
Net change +15<br />
<br />
<br />
<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 7866 (33.8%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 10792 (46.4%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 4615 (19.8%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB/Swiss-Prot accessions 3496 (15.0%)<br />
UniProtKB/TrEMBL accessions 19225 (82.6%)<br />
<br />
<br />
<br />
<br />
GeneModel correction progress WS174 -&gt; WS175<br />
-----------------------------------------<br />
Confirmed introns not in a CDS gene model;<br />
<br />
+---------+--------+<br />
| Introns | Change |<br />
+---------+--------+<br />
Cambridge | 173 | -13 |<br />
St Louis | 212 | -3 |<br />
+---------+--------+<br />
<br />
<br />
Members of known repeat families that overlap predicted exons;<br />
<br />
+---------+--------+<br />
| Repeats | Change |<br />
+---------+--------+<br />
Cambridge | 6 | 0 |<br />
St Louis | 6 | 0 |<br />
+---------+--------+<br />
<br />
<br />
<br />
Synchronisation with GenBank / EMBL:<br />
------------------------------------<br />
<br />
No synchronisation issues<br />
<br />
<br />
There are no gaps remaining in the genome sequence<br />
---------------<br />
For more info mail worm@sanger.ac.uk<br />
-===================================================================================-<br />
<br />
<br />
<br />
New Data:<br />
---------<br />
Database cross references to miRBase have been added to 131 genes.<br />
<br />
Genome sequence updates:<br />
-----------------------<br />
<br />
<br />
New Fixes:<br />
----------<br />
<br />
<br />
Known Problems:<br />
---------------<br />
<br />
<br />
Other Changes:<br />
--------------<br />
<br />
Proposed Changes / Forthcoming Data:<br />
-------------------------------------<br />
<br />
<br />
Model Changes:<br />
------------------------------------<br />
Added tags to ?Person and ?Paper to enable recording of negative connections ie Mr X did NOT contribue to this paper.<br />
<br />
Added Map_evidence to ?Transgene so that the paper that mapping data is taken from can be attributed<br />
<br />
Added a tags to ?Expr_pattern and  ?Expression_cluster to handle Localizome data<br />
<br />
Changes in the ?Interaction model as proposed by Andrei. Added #Interactor_info and #Interaction_info<br />
<br />
Directed_Y1H in YH class<br />
<br />
-===================================================================================-<br />
<br />
<br />
Quick installation guide for UNIX/Linux systems<br />
-----------------------------------------------<br />
<br />
1. Create a new directory to contain your copy of WormBase,<br />
e.g. /users/yourname/wormbase<br />
<br />
2. Unpack and untar all of the database.*.tar.gz files into<br />
this directory. You will need approximately 2-3 Gb of disk space.<br />
<br />
3. Obtain and install a suitable acedb binary for your system<br />
(available from www.acedb.org).<br />
<br />
4. Use the acedb 'xace' program to open your database, e.g.<br />
type 'xace /users/yourname/wormbase' at the command prompt.<br />
<br />
5. See the acedb website for more information about acedb and<br />
using xace.<br />
<br />
____________ END _____________<br />
</nowiki></div>
Tharris