I just checked this and can confirm that the search feature of GBrowse 1.70 is broken when you give multiple features the same name. You can work around this by giving them a series of distinct names, such as MA-00016283.1, MA-00016283.2, etc, and then giving them all the same "Alias" attribute of MA-00016283.<br>
<br>The problem does not exist in GBrowse 2.0.<br><br>Lincoln<br><br><div class="gmail_quote">On Thu, Sep 3, 2009 at 5:59 AM, abdul pichon <span dir="ltr"><<a href="mailto:abdul.pichon@gmail.com">abdul.pichon@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Hello</div>
<div> </div>
<div>Does anyone have any idea ?</div>
<div> </div>
<div>I tried a search within this GGB, with public access :</div>
<div><a href="http://gbrowse.maizegdb.org/gbrowse/cgi-bin/gbrowse/maize/#search" target="_blank">http://gbrowse.maizegdb.org/gbrowse/cgi-bin/gbrowse/maize/#search</a><br><br>When I search for the string CL34420_2_ov (a marker) , I retrieve 7 results, and only one is located on Chr1.</div>
<div>But the marker CL34420_2_ov has as least TWO locations on Chr1 : <font size="2" face="Helv"><font size="2" face="Helv">
<p dir="ltr">Chr1:247489200..247494100</p></font></font><font size="2" face="Helv"><font size="2" face="Helv"></font></font></div>
<div>and </div>
<div><font size="2" face="Helv"><font size="2" face="Helv">
<p dir="ltr">Chr1:251487000..251494000</p>
<p dir="ltr">The bug is that only one result is returned for one reference sequence. GGB seems to think that it is not possible that a feature can have more than one location on the same sequence.</p>
<p dir="ltr">Thank you</p>
<p dir="ltr">AP</p></font></font></div>
<div class="gmail_quote">2009/8/27 abdul pichon <span dir="ltr"><<a href="mailto:abdul.pichon@gmail.com" target="_blank">abdul.pichon@gmail.com</a>></span><div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">
<div>Hello Dave</div>
<div> </div>
<div>When I search for MA-00016283, it retrieves only ten results. I cant' see any pattern to those 10, because the search string is exactly the same as the tag Name=MA-00016283 are in my GFF file.</div>
<div>But it seems to be only the "first" feature from the begining of each chromosome.</div>
<div> </div>
<div>I have loaded the same GFF file I provided in my first message within the WebGbrowse (<a href="http://webgbrowse.cgb.indiana.edu/webgbrowse/cgi-bin/uploadData" target="_blank">http://webgbrowse.cgb.indiana.edu/webgbrowse/cgi-bin/uploadData</a>), here is attached a screenshot of the result of the search page. This GGB displays only 10 results, just like my own GGB.</div>
<div> </div>
<div> </div>
<div>Thanks</div>
<div>AP.<br><br></div>
<div class="gmail_quote">2009/8/27 Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com" target="_blank">gmodhelp@googlemail.com</a>></span>
<div>
<div></div>
<div><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Hi Abdul,<br><br>I admit that I have no idea what is going on here. I can't see why it<br>
would return 10, but not all of them. Which 10 features are returned<br>
when you do the search? Is there any pattern to those 10?<br><br>Dave C.<br>
<div>
<div></div>
<div><br>On Fri, Aug 21, 2009 at 7:27 AM, abdul pichon<<a href="mailto:abdul.pichon@gmail.com" target="_blank">abdul.pichon@gmail.com</a>> wrote:<br>> Hello<br>><br>> I have a very simple GGB (Generic genome browser version 1.7) database<br>
> (using Bio::DB::SeqFeature::Store adaptor)<br>><br>> I've loaded two files (using bp_seqfeature_load.pl)<br>><br>> Is there something wrong with my gff ?<br>><br>> Because when I use the landmark MA-00016283 in the search box, I do not<br>
> retrieve all my features (50) but only 10, one for each chromosome.<br>><br>> Could you please help me ?<br>><br>> Thank You.<br>><br>> Abdul.<br>><br>><br>> Here are the two files I used :<br>
><br>> ##gff-version 3<br>> Chr1 Arizona chromosome 1 300239041 . .<br>> . ID=Chr1;Name=Chr1<br>> Chr2 Arizona chromosome 1 234752839 . .<br>> . ID=Chr2;Name=Chr2<br>
> Chr3 Arizona chromosome 1 230558137 . .<br>> . ID=Chr3;Name=Chr3<br>> Chr4 Arizona chromosome 1 247095508 . .<br>> . ID=Chr4;Name=Chr4<br>> Chr5 Arizona chromosome 1 216915529 . .<br>
> . ID=Chr5;Name=Chr5<br>> Chr6 Arizona chromosome 1 169254300 . .<br>> . ID=Chr6;Name=Chr6<br>> Chr7 Arizona chromosome 1 170974187 . .<br>> . ID=Chr7;Name=Chr7<br>
> Chr8 Arizona chromosome 1 174515299 . .<br>> . ID=Chr8;Name=Chr8<br>> Chr9 Arizona chromosome 1 152350485 . .<br>> . ID=Chr9;Name=Chr9<br>> Chr10 Arizona chromosome 1 149686045 . .<br>
> . ID=Chr10;Name=Chr10<br>> Chr0 Arizona chromosome 1 14680007 . .<br>> . ID=Chr0;Name=Chr0<br>> Chr10 MAIZE match 45134481 45134645 126 +<br>> . ID=Chr10:MA-00016283:45134481:45134645;Name=MA-00016283<br>
> Chr10 MAIZE match 94683635 94683792 127 +<br>> . ID=Chr10:MA-00016283:94683635:94683792;Name=MA-00016283<br>> Chr1 MAIZE match 118774466 118774630 118 +<br>
> . ID=Chr1:MA-00016283:118774466:118774630;Name=MA-00016283<br>
> Chr1 MAIZE match 225743879 225744044 123 -<br>> . ID=Chr1:MA-00016283:225743879:225744044;Name=MA-00016283<br>> Chr1 MAIZE match 235087848 235088012 134 -<br>
> . ID=Chr1:MA-00016283:235087848:235088012;Name=MA-00016283<br>> Chr1 MAIZE match 254710388 254710552 118 +<br>> . ID=Chr1:MA-00016283:254710388:254710552;Name=MA-00016283<br>
> Chr1 MAIZE match 277970259 277970423 130 -<br>
> . ID=Chr1:MA-00016283:277970259:277970423;Name=MA-00016283<br>> Chr1 MAIZE match 28410936 28411100 118 +<br>> . ID=Chr1:MA-00016283:28410936:28411100;Name=MA-00016283<br>> Chr1 MAIZE match 63794387 63794551 118 +<br>
> . ID=Chr1:MA-00016283:63794387:63794551;Name=MA-00016283<br>> Chr1 MAIZE match 78469620 78469784 118 -<br>> . ID=Chr1:MA-00016283:78469620:78469784;Name=MA-00016283<br>> Chr2 MAIZE match 211319455 211319619 122 +<br>
> . ID=Chr2:MA-00016283:211319455:211319619;Name=MA-00016283<br>> Chr2 MAIZE match 34588170 34588334 118 +<br>> . ID=Chr2:MA-00016283:34588170:34588334;Name=MA-00016283<br>> Chr2 MAIZE match 503312 503476 130 + .<br>
> ID=Chr2:MA-00016283:503312:503476;Name=MA-00016283<br>> Chr3 MAIZE match 11352185 11352349 118 -<br>> . ID=Chr3:MA-00016283:11352185:11352349;Name=MA-00016283<br>> Chr3 MAIZE match 123892245 123892404 123 +<br>
> . ID=Chr3:MA-00016283:123892245:123892404;Name=MA-00016283<br>> Chr3 MAIZE match 124056825 124056984 123 +<br>> . ID=Chr3:MA-00016283:124056825:124056984;Name=MA-00016283<br>
> Chr3 MAIZE match 219449043 219449207 118 +<br>
> . ID=Chr3:MA-00016283:219449043:219449207;Name=MA-00016283<br>> Chr3 MAIZE match 227216128 227216292 118 +<br>> . ID=Chr3:MA-00016283:227216128:227216292;Name=MA-00016283<br>
> Chr3 MAIZE match 39803860 39804024 126 +<br>
> . ID=Chr3:MA-00016283:39803860:39804024;Name=MA-00016283<br>> Chr3 MAIZE match 50892943 50893107 118 -<br>> . ID=Chr3:MA-00016283:50892943:50893107;Name=MA-00016283<br>> Chr3 MAIZE match 50922379 50922543 118 +<br>
> . ID=Chr3:MA-00016283:50922379:50922543;Name=MA-00016283<br>> Chr3 MAIZE match 65682357 65682521 130 +<br>> . ID=Chr3:MA-00016283:65682357:65682521;Name=MA-00016283<br>> Chr3 MAIZE match 98389305 98389469 122 +<br>
> . ID=Chr3:MA-00016283:98389305:98389469;Name=MA-00016283<br>> Chr4 MAIZE match 138809790 138809954 126 -<br>> . ID=Chr4:MA-00016283:138809790:138809954;Name=MA-00016283<br>> Chr4 MAIZE match 88854586 88854750 122 -<br>
> . ID=Chr4:MA-00016283:88854586:88854750;Name=MA-00016283<br>> Chr5 MAIZE match 139403345 139403504 127 -<br>> . ID=Chr5:MA-00016283:139403345:139403504;Name=MA-00016283<br>> Chr5 MAIZE match 148064749 148064913 134 +<br>
> . ID=Chr5:MA-00016283:148064749:148064913;Name=MA-00016283<br>> Chr5 MAIZE match 148066166 148066330 118 +<br>> . ID=Chr5:MA-00016283:148066166:148066330;Name=MA-00016283<br>
> Chr5 MAIZE match 172304226 172304390 126 +<br>
> . ID=Chr5:MA-00016283:172304226:172304390;Name=MA-00016283<br>> Chr5 MAIZE match 21175948 21176112 118 -<br>> . ID=Chr5:MA-00016283:21175948:21176112;Name=MA-00016283<br>> Chr5 MAIZE match 54628946 54629110 130 +<br>
> . ID=Chr5:MA-00016283:54628946:54629110;Name=MA-00016283<br>> Chr6 MAIZE match 112762222 112762386 126 +<br>> . ID=Chr6:MA-00016283:112762222:112762386;Name=MA-00016283<br>> Chr6 MAIZE match 158849431 158849595 122 +<br>
> . ID=Chr6:MA-00016283:158849431:158849595;Name=MA-00016283<br>> Chr6 MAIZE match 167302386 167302550 122 -<br>> . ID=Chr6:MA-00016283:167302386:167302550;Name=MA-00016283<br>
> Chr6 MAIZE match 25988843 25989007 130 -<br>
> . ID=Chr6:MA-00016283:25988843:25989007;Name=MA-00016283<br>> Chr6 MAIZE match 67879539 67879703 126 -<br>> . ID=Chr6:MA-00016283:67879539:67879703;Name=MA-00016283<br>> Chr7 MAIZE match 3334950 3335114 122 - .<br>
> ID=Chr7:MA-00016283:3334950:3335114;Name=MA-00016283<br>> Chr7 MAIZE match 76146084 76146248 130 +<br>> . ID=Chr7:MA-00016283:76146084:76146248;Name=MA-00016283<br>> Chr7 MAIZE match 79672906 79673070 134 -<br>
> . ID=Chr7:MA-00016283:79672906:79673070;Name=MA-00016283<br>> Chr8 MAIZE match 132498602 132498766 130 -<br>> . ID=Chr8:MA-00016283:132498602:132498766;Name=MA-00016283<br>> Chr8 MAIZE match 47600399 47600563 126 -<br>
> . ID=Chr8:MA-00016283:47600399:47600563;Name=MA-00016283<br>> Chr8 MAIZE match 53286720 53286884 130 +<br>> . ID=Chr8:MA-00016283:53286720:53286884;Name=MA-00016283<br>> Chr8 MAIZE match 57653070 57653234 126 +<br>
> . ID=Chr8:MA-00016283:57653070:57653234;Name=MA-00016283<br>> Chr9 MAIZE match 13591217 13591381 130 +<br>> . ID=Chr9:MA-00016283:13591217:13591381;Name=MA-00016283<br>> Chr9 MAIZE match 29042095 29042259 130 +<br>
> . ID=Chr9:MA-00016283:29042095:29042259;Name=MA-00016283<br>> Chr9 MAIZE match 63849519 63849683 130 -<br>> . ID=Chr9:MA-00016283:63849519:63849683;Name=MA-00016283<br>> Chr9 MAIZE match 70247484 70247648 122 +<br>
> . ID=Chr9:MA-00016283:70247484:70247648;Name=MA-00016283<br>> Chr9 MAIZE match 72578083 72578247 126 +<br>> . ID=Chr9:MA-00016283:72578083:72578247;Name=MA-00016283<br>><br>
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</font></blockquote></div></div></div><br></blockquote></div></div></div><br>
</blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
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