<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">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 face="Helv" size="2"><font face="Helv" size="2">
<p dir="ltr">Chr1:247489200..247494100</p></font></font><font face="Helv" size="2"><font face="Helv" size="2"></font></font></div>
<div>and </div>
<div><font face="Helv" size="2"><font face="Helv" size="2">
<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">abdul.pichon@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<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 class="h5"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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>
</div></div>> ------------------------------------------------------------------------------<br>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day<br>> trial. Simplify your report design, integration and deployment - and focus<br>
> on<br>> what you do best, core application coding. Discover what's new with<br>> Crystal Reports now. <a href="http://p.sf.net/sfu/bobj-july" target="_blank">http://p.sf.net/sfu/bobj-july</a><br>> _______________________________________________<br>
> Gmod-gbrowse mailing list<br>> <a href="mailto:Gmod-gbrowse@lists.sourceforge.net" target="_blank">Gmod-gbrowse@lists.sourceforge.net</a><br>> <a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
><br>><br><font color="#888888"><br><br><br>--<br>* Please keep responses on the list!<br>* Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
</font></blockquote></div></div></div><br></blockquote></div><br>