https://wiki.wormbase.org/index.php?title=WS187&feed=atom&action=history
WS187 - Revision history
2024-03-29T12:31:17Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://wiki.wormbase.org/index.php?title=WS187&diff=13229&oldid=prev
Pdavis at 16:43, 21 December 2011
2011-12-21T16:43:00Z
<p></p>
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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 16:43, 21 December 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l138" >Line 138:</td>
<td colspan="2" class="diff-lineno">Line 138:</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>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>
<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;"></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;"></td></tr>
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Pdavis
https://wiki.wormbase.org/index.php?title=WS187&diff=950&oldid=prev
Pdavis at 05:50, 3 April 2008
2008-04-03T05:50:44Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 05:50, 3 April 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</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;"></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;"></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>WS187 was built by Gary Williams</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>WS187 was built by Gary Williams <ins class="diffchange diffchange-inline">(gw3@sanger.ac.uk)</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=WS187&diff=603&oldid=prev
Gwilliams: New page: = Release Notes = <pre> New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008 WS187 was built by Gary Williams ===========================================...
2008-01-29T05:11:09Z
<p>New page: = Release Notes = <pre> New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008 WS187 was built by Gary Williams ===========================================...</p>
<p><b>New page</b></p><div>= Release Notes =<br />
<pre><br />
New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008<br />
<br />
<br />
WS187 was built by Gary Williams<br />
======================================================================<br />
<br />
This directory includes:<br />
i) database.WS187.*.tar.gz - compressed data for new release<br />
ii) models.wrm.WS187 - the latest database schema (also in above database files)<br />
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)<br />
iv) WS187-WS186.dbcomp - log file reporting difference from last release<br />
v) wormpep187.tar.gz - full Wormpep distribution corresponding to WS187<br />
vi) wormrna187.tar.gz - latest WormRNA release containing non-coding RNA's in the genome<br />
vii) confirmed_genes.WS187.gz - DNA sequences of all genes confirmed by EST &/or cDNA<br />
viii) cDNA2orf.WS187.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)<br />
ix) gene_interpolated_map_positions.WS187.gz - Interpolated map positions for each coding/RNA gene<br />
x) clone_interpolated_map_positions.WS187.gz - Interpolated map positions for each clone<br />
xi) best_blastp_hits.WS187.gz - for each C. elegans WormPep protein, lists Best blastp match to<br />
human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.<br />
xii) best_blastp_hits_brigprot.WS187.gz - for each C. briggsae protein, lists Best blastp match to<br />
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.<br />
xiii) geneIDs.WS187.gz - list of all current gene identifiers with CGC & molecular names (when known)<br />
xiv) PCR_product2gene.WS187.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 />
WS187 WS186 change<br />
----------------------------------------------<br />
a 32365950 32365950 +0<br />
c 17779886 17779886 +0<br />
g 17756037 17756037 +0<br />
t 32365750 32365750 +0<br />
n 0 0 +0<br />
- 0 0 +0<br />
<br />
Total 100267623 100267623 +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 29647)<br />
------------------------------------------<br />
Molecular_info 27947 (94.3%)<br />
Concise_description 5147 (17.4%)<br />
Reference 7586 (25.6%)<br />
WormBase_approved Gene name 15172 (51.2%)<br />
RNAi_result 20736 (69.9%)<br />
Microarray_results 19963 (67.3%)<br />
SAGE_transcript 18732 (63.2%)<br />
<br />
<br />
<br />
<br />
Wormpep data set:<br />
----------------------------<br />
<br />
There are 20170 CDS in autoace, 23662 when counting 3492 alternate splice forms.<br />
<br />
The 23662 sequences contain base pairs in total.<br />
<br />
Modified entries 50<br />
Deleted entries 18<br />
New entries 35<br />
Reappeared entries 0<br />
<br />
Net change +17<br />
<br />
<br />
<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 8337 (35.2%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 10964 (46.3%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 4361 (18.4%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB/Swiss-Prot accessions 3678 (15.5%)<br />
UniProtKB/TrEMBL accessions 19707 (83.3%)<br />
<br />
<br />
<br />
Status of entries: Protein_ID's in EMBL<br />
---------------------------------------<br />
Protein_id 23385 (98.8%)<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis elegans entries with WormBase-approved Gene name 13522<br />
<br />
<br />
GeneModel correction progress WS186 -> WS187<br />
-----------------------------------------<br />
Confirmed introns not in a CDS gene model;<br />
<br />
+---------+--------+<br />
| Introns | Change |<br />
+---------+--------+<br />
Cambridge | 127 | 3 |<br />
St Louis | 404 | -68 |<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 />
<br />
Blast database versions:<br />
ipi_human_01_08.pep<br />
yeast28.pep<br />
<br />
TreeFam IDs are now imported for multiple isoforms of a gene.<br />
<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 />
<br />
added Variation_evidence to Evidence hash<br />
<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 />
</pre></div>
Gwilliams