[Gmod-help] Re: [Gmod-gbrowse] Searching in gbrowse does not retrieve all features
abdul pichon
abdul.pichon at gmail.com
Thu Sep 3 05:59:29 EDT 2009
Hello
Does anyone have any idea ?
I tried a search within this GGB, with public access :
http://gbrowse.maizegdb.org/gbrowse/cgi-bin/gbrowse/maize/#search
When I search for the string CL34420_2_ov (a marker) , I retrieve 7 results,
and only one is located on Chr1.
But the marker CL34420_2_ov has as least TWO locations on Chr1 :
Chr1:247489200..247494100
and
Chr1:251487000..251494000
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.
Thank you
AP
2009/8/27 abdul pichon <abdul.pichon at gmail.com>
> Hello Dave
>
> 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.
> But it seems to be only the "first" feature from the begining of each
> chromosome.
>
> I have loaded the same GFF file I provided in my first message within the
> WebGbrowse (
> http://webgbrowse.cgb.indiana.edu/webgbrowse/cgi-bin/uploadData), here is
> attached a screenshot of the result of the search page. This GGB displays
> only 10 results, just like my own GGB.
>
>
> Thanks
> AP.
>
> 2009/8/27 Dave Clements, GMOD Help Desk <gmodhelp at googlemail.com>
>
> Hi Abdul,
>>
>> I admit that I have no idea what is going on here. I can't see why it
>> would return 10, but not all of them. Which 10 features are returned
>> when you do the search? Is there any pattern to those 10?
>>
>> Dave C.
>>
>> On Fri, Aug 21, 2009 at 7:27 AM, abdul pichon<abdul.pichon at gmail.com>
>> wrote:
>> > Hello
>> >
>> > I have a very simple GGB (Generic genome browser version 1.7) database
>> > (using Bio::DB::SeqFeature::Store adaptor)
>> >
>> > I've loaded two files (using bp_seqfeature_load.pl)
>> >
>> > Is there something wrong with my gff ?
>> >
>> > Because when I use the landmark MA-00016283 in the search box, I do not
>> > retrieve all my features (50) but only 10, one for each chromosome.
>> >
>> > Could you please help me ?
>> >
>> > Thank You.
>> >
>> > Abdul.
>> >
>> >
>> > Here are the two files I used :
>> >
>> > ##gff-version 3
>> > Chr1 Arizona chromosome 1 300239041 . .
>> > . ID=Chr1;Name=Chr1
>> > Chr2 Arizona chromosome 1 234752839 . .
>> > . ID=Chr2;Name=Chr2
>> > Chr3 Arizona chromosome 1 230558137 . .
>> > . ID=Chr3;Name=Chr3
>> > Chr4 Arizona chromosome 1 247095508 . .
>> > . ID=Chr4;Name=Chr4
>> > Chr5 Arizona chromosome 1 216915529 . .
>> > . ID=Chr5;Name=Chr5
>> > Chr6 Arizona chromosome 1 169254300 . .
>> > . ID=Chr6;Name=Chr6
>> > Chr7 Arizona chromosome 1 170974187 . .
>> > . ID=Chr7;Name=Chr7
>> > Chr8 Arizona chromosome 1 174515299 . .
>> > . ID=Chr8;Name=Chr8
>> > Chr9 Arizona chromosome 1 152350485 . .
>> > . ID=Chr9;Name=Chr9
>> > Chr10 Arizona chromosome 1 149686045 . .
>> > . ID=Chr10;Name=Chr10
>> > Chr0 Arizona chromosome 1 14680007 . .
>> > . ID=Chr0;Name=Chr0
>> > Chr10 MAIZE match 45134481 45134645 126 +
>> > . ID=Chr10:MA-00016283:45134481:45134645;Name=MA-00016283
>> > Chr10 MAIZE match 94683635 94683792 127 +
>> > . ID=Chr10:MA-00016283:94683635:94683792;Name=MA-00016283
>> > Chr1 MAIZE match 118774466 118774630 118 +
>> > . ID=Chr1:MA-00016283:118774466:118774630;Name=MA-00016283
>> > Chr1 MAIZE match 225743879 225744044 123 -
>> > . ID=Chr1:MA-00016283:225743879:225744044;Name=MA-00016283
>> > Chr1 MAIZE match 235087848 235088012 134 -
>> > . ID=Chr1:MA-00016283:235087848:235088012;Name=MA-00016283
>> > Chr1 MAIZE match 254710388 254710552 118 +
>> > . ID=Chr1:MA-00016283:254710388:254710552;Name=MA-00016283
>> > Chr1 MAIZE match 277970259 277970423 130 -
>> > . ID=Chr1:MA-00016283:277970259:277970423;Name=MA-00016283
>> > Chr1 MAIZE match 28410936 28411100 118 +
>> > . ID=Chr1:MA-00016283:28410936:28411100;Name=MA-00016283
>> > Chr1 MAIZE match 63794387 63794551 118 +
>> > . ID=Chr1:MA-00016283:63794387:63794551;Name=MA-00016283
>> > Chr1 MAIZE match 78469620 78469784 118 -
>> > . ID=Chr1:MA-00016283:78469620:78469784;Name=MA-00016283
>> > Chr2 MAIZE match 211319455 211319619 122 +
>> > . ID=Chr2:MA-00016283:211319455:211319619;Name=MA-00016283
>> > Chr2 MAIZE match 34588170 34588334 118 +
>> > . ID=Chr2:MA-00016283:34588170:34588334;Name=MA-00016283
>> > Chr2 MAIZE match 503312 503476 130 + .
>> > ID=Chr2:MA-00016283:503312:503476;Name=MA-00016283
>> > Chr3 MAIZE match 11352185 11352349 118 -
>> > . ID=Chr3:MA-00016283:11352185:11352349;Name=MA-00016283
>> > Chr3 MAIZE match 123892245 123892404 123 +
>> > . ID=Chr3:MA-00016283:123892245:123892404;Name=MA-00016283
>> > Chr3 MAIZE match 124056825 124056984 123 +
>> > . ID=Chr3:MA-00016283:124056825:124056984;Name=MA-00016283
>> > Chr3 MAIZE match 219449043 219449207 118 +
>> > . ID=Chr3:MA-00016283:219449043:219449207;Name=MA-00016283
>> > Chr3 MAIZE match 227216128 227216292 118 +
>> > . ID=Chr3:MA-00016283:227216128:227216292;Name=MA-00016283
>> > Chr3 MAIZE match 39803860 39804024 126 +
>> > . ID=Chr3:MA-00016283:39803860:39804024;Name=MA-00016283
>> > Chr3 MAIZE match 50892943 50893107 118 -
>> > . ID=Chr3:MA-00016283:50892943:50893107;Name=MA-00016283
>> > Chr3 MAIZE match 50922379 50922543 118 +
>> > . ID=Chr3:MA-00016283:50922379:50922543;Name=MA-00016283
>> > Chr3 MAIZE match 65682357 65682521 130 +
>> > . ID=Chr3:MA-00016283:65682357:65682521;Name=MA-00016283
>> > Chr3 MAIZE match 98389305 98389469 122 +
>> > . ID=Chr3:MA-00016283:98389305:98389469;Name=MA-00016283
>> > Chr4 MAIZE match 138809790 138809954 126 -
>> > . ID=Chr4:MA-00016283:138809790:138809954;Name=MA-00016283
>> > Chr4 MAIZE match 88854586 88854750 122 -
>> > . ID=Chr4:MA-00016283:88854586:88854750;Name=MA-00016283
>> > Chr5 MAIZE match 139403345 139403504 127 -
>> > . ID=Chr5:MA-00016283:139403345:139403504;Name=MA-00016283
>> > Chr5 MAIZE match 148064749 148064913 134 +
>> > . ID=Chr5:MA-00016283:148064749:148064913;Name=MA-00016283
>> > Chr5 MAIZE match 148066166 148066330 118 +
>> > . ID=Chr5:MA-00016283:148066166:148066330;Name=MA-00016283
>> > Chr5 MAIZE match 172304226 172304390 126 +
>> > . ID=Chr5:MA-00016283:172304226:172304390;Name=MA-00016283
>> > Chr5 MAIZE match 21175948 21176112 118 -
>> > . ID=Chr5:MA-00016283:21175948:21176112;Name=MA-00016283
>> > Chr5 MAIZE match 54628946 54629110 130 +
>> > . ID=Chr5:MA-00016283:54628946:54629110;Name=MA-00016283
>> > Chr6 MAIZE match 112762222 112762386 126 +
>> > . ID=Chr6:MA-00016283:112762222:112762386;Name=MA-00016283
>> > Chr6 MAIZE match 158849431 158849595 122 +
>> > . ID=Chr6:MA-00016283:158849431:158849595;Name=MA-00016283
>> > Chr6 MAIZE match 167302386 167302550 122 -
>> > . ID=Chr6:MA-00016283:167302386:167302550;Name=MA-00016283
>> > Chr6 MAIZE match 25988843 25989007 130 -
>> > . ID=Chr6:MA-00016283:25988843:25989007;Name=MA-00016283
>> > Chr6 MAIZE match 67879539 67879703 126 -
>> > . ID=Chr6:MA-00016283:67879539:67879703;Name=MA-00016283
>> > Chr7 MAIZE match 3334950 3335114 122 - .
>> > ID=Chr7:MA-00016283:3334950:3335114;Name=MA-00016283
>> > Chr7 MAIZE match 76146084 76146248 130 +
>> > . ID=Chr7:MA-00016283:76146084:76146248;Name=MA-00016283
>> > Chr7 MAIZE match 79672906 79673070 134 -
>> > . ID=Chr7:MA-00016283:79672906:79673070;Name=MA-00016283
>> > Chr8 MAIZE match 132498602 132498766 130 -
>> > . ID=Chr8:MA-00016283:132498602:132498766;Name=MA-00016283
>> > Chr8 MAIZE match 47600399 47600563 126 -
>> > . ID=Chr8:MA-00016283:47600399:47600563;Name=MA-00016283
>> > Chr8 MAIZE match 53286720 53286884 130 +
>> > . ID=Chr8:MA-00016283:53286720:53286884;Name=MA-00016283
>> > Chr8 MAIZE match 57653070 57653234 126 +
>> > . ID=Chr8:MA-00016283:57653070:57653234;Name=MA-00016283
>> > Chr9 MAIZE match 13591217 13591381 130 +
>> > . ID=Chr9:MA-00016283:13591217:13591381;Name=MA-00016283
>> > Chr9 MAIZE match 29042095 29042259 130 +
>> > . ID=Chr9:MA-00016283:29042095:29042259;Name=MA-00016283
>> > Chr9 MAIZE match 63849519 63849683 130 -
>> > . ID=Chr9:MA-00016283:63849519:63849683;Name=MA-00016283
>> > Chr9 MAIZE match 70247484 70247648 122 +
>> > . ID=Chr9:MA-00016283:70247484:70247648;Name=MA-00016283
>> > Chr9 MAIZE match 72578083 72578247 126 +
>> > . ID=Chr9:MA-00016283:72578083:72578247;Name=MA-00016283
>> >
>> >
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