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Hi Gang Chen,<br>
<br>
It looks like the default Esnembl search plugin is not compatible
with Ensembl Bacteria when searching a single species. If you are
mirroring the Ensembl Bacteria data you may want to try connecting
to the EBI search webservice using the EBEye search plugin. <br>
<br>
The plugin is in CVS here
<a class="moz-txt-link-freetext" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/eg-plugins/ebeye-search/?root=ensembl">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/eg-plugins/ebeye-search/?root=ensembl</a><br>
<br>
To install...<br>
<br>
1. check out the plugin code into you eg-plugins dir E.g.<br>
<br>
$ cd <your-server-root><br>
$ cvs co -r branch-ensemblgenomes-16-69 eg-plugins/ebeye-search<br>
<br>
2. add (or un-comment) the following line in your plugins file
(<your-server-root>/conf/Plugins.pm)<br>
<br>
'EG::EBEyeSearch' =>
$SiteDefs::ENSEMBL_SERVERROOT.'/eg-plugins/ebeye-search',<br>
<font face="verdana, sans-serif" size="1"></font><br>
The EG::EBEyeSearch plugin should be above the EG::Bacteria plugin
in the file.<br>
<br>
3. configure the search endpoint by adding the following lines to
<your-server-root>/my-plugins/conf/ini-files/DEFAULTS.ini<br>
<br>
[general]<br>
EBEYE_ENDPOINT = <a class="moz-txt-link-freetext" href="http://www.ebi.ac.uk/ebisearch/service.ebi">http://www.ebi.ac.uk/ebisearch/service.ebi</a><br>
<br>
4. Restart your server.<br>
<br>
You should now have full search functionality.<br>
<br>
Please let me know if this solves your problem of if there is
anything else you need.<br>
<br>
Thanks<br>
Nick<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 04/01/2013 02:32, 陈岗 wrote:<br>
</div>
<blockquote
cite="mid:CABjKtWY89a46dV=09YRRQb2zqyZ5+Eqdc7-qzOAFQ1pc=0HvSw@mail.gmail.com"
type="cite">
<div dir="ltr">Hi All
<div><br>
</div>
<div>Our EnsemblGenomes mirror suffers a search error. For
instance, search dnaA in species Escherichia coli K12, the
mirror returns 12 entries. </div>
<div><br>
</div>
<div>
<div>Gene: EBESCG00000003429 [Region in detail]</div>
<div>Gene: EBESCG00000007452 [Region in detail]</div>
<div>Gene: EBESCG00000013460 [Region in detail]</div>
<div>Gene: EBESCG00000018762 [Region in detail]</div>
<div>Gene: EBESCG00000023601 [Region in detail]</div>
<div>Gene: EBESCG00000031974 [Region in detail]</div>
<div>Gene: EBESCG00000037518 [Region in detail]</div>
<div>Gene: EBESCG00000048558 [Region in detail]</div>
<div>Gene: EBESCG00000052321 [Region in detail]</div>
<div>Gene: EBESCG00000057553 [Region in detail]</div>
<div>Gene: EBESCG00000003435 [Region in detail]</div>
<div>Gene: EBESCG00000002586 [Region in detail]</div>
</div>
<div><br>
</div>
<div>However, some linkages of these entries are unavailable,
report a internal page error, including </div>
<div>EBESCG00000007452
<div>EBESCG00000013460</div>
<div>EBESCG00000018762</div>
<div>EBESCG00000023601 and so on.</div>
<div><br>
</div>
<div>I checked above IDs from
tables ensembl_compara_bacteria_16_69.member
and ensembl_compara_bacteria_16_69.genome_db, they are not
belong to species Escherichia coli K12,
but e_coli_atcc_8739, e_coli_atcc_27325, e_coli_o139_h28, e_coli_edl933
respectively.</div>
<div><br>
</div>
<div>If change the URLs which return the internal error with
above names, they work correctly. For example, change </div>
<div><a moz-do-not-send="true"
href="http://172.16.10.16:8899/e_coli_k12/Gene/Summary?g=EBESCG00000007452;db=core"
target="_blank">http://172.16.10.16:8899/e_coli_k12/Gene/Summary?g=EBESCG00000007452;db=core</a></div>
<div>to </div>
<div><a moz-do-not-send="true"
href="http://172.16.10.16:8899/e_coli_atcc_8739/Gene/Summary?db=core;g=EBESCG00000007452"
target="_blank">http://172.16.10.16:8899/e_coli_atcc_8739/Gene/Summary?db=core;g=EBESCG00000007452</a><br>
</div>
<div>
<br>
</div>
<div>Therefore, the search error is caused by wrong species
name which is applied as a part of URL. Could you fix the
error? </div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
<div>
-- <br>
</div>
<div><font face="verdana, sans-serif" size="1">Gang Chen</font></div>
<div><font face="verdana, sans-serif" size="1">TILSI</font></div>
<div><font face="verdana, sans-serif" size="1"><span style="">Taicang
Institute For Life Science Information</span><br
style="">
<span style="">Address: A2/162, Renmin South Road,
Taicang, 215400, Jiangsu Province, P.R.China</span><br
style="">
<span style="">Phone:（+86）512-82782588</span></font></div>
</div>
</div>
<br>
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<br>
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</pre>
</blockquote>
<br>
<br>
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