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webGbrowse

Ashley Lu

Hi everyone,

 

I am completely new to GBrowse, and trying tying  to get my head around this toll.

So I have a genbank file, and I used the bp_genbank2gff3.pl to convert it to a gff format.

and I have trouble displaying this gff file on webGBrowse.

 

I’ve use the ‘gff3-validator’ tool to check the format of the gff file, and nothing unusual.

Also I’ve noticed that when I tried to do a search using column 1 of the gff file, sometimes it appears as ‘landmark name not recognised’,

and sometimes it did manage to find the landmark by giving a message ‘The following 3 regions match your request’,  but either ways, no image is produced.

 

Can you please have a look at this gff file and see what might be causing trouble?

 

Thank you very mcuh

 

Ashley Lu

Research Associate

 

Plant & Food Research

 

+6421921186
[hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited

 

Postal Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Private Bag 4704, , Christchurch, 8140, New Zealand
Physical Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Gerald Street, Lincoln, 7608, New Zealand

 

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Re: webGbrowse

Ram Podicheti-2
<base href="x-msg://109/">
Hi Ashley,
Can you try updating the first line of your GFF file setting the ID and Name of the contig to the sequence ID?

For eg: 

C01_001 Genbank contig 1 4659 . + 1 ID=C01_001;Dbxref=taxon:1095103;Name=C01_001;

ID and Name define the SeqID which identifies the landmark you are trying to display.

Please let me know how it goes.

Cheers,

Ram


On May 15, 2012, at 9:35 PM, Ashley Lu wrote:

Hi everyone,
 
I am completely new to GBrowse, and trying tying  to get my head around this toll.
So I have a genbank file, and I used the bp_genbank2gff3.pl to convert it to a gff format.
and I have trouble displaying this gff file on webGBrowse.
 
I’ve use the ‘gff3-validator’ tool to check the format of the gff file, and nothing unusual.
Also I’ve noticed that when I tried to do a search using column 1 of the gff file, sometimes it appears as ‘landmark name not recognised’,
and sometimes it did manage to find the landmark by giving a message ‘The following 3 regions match your request’,  but either ways, no image is produced.
 
Can you please have a look at this gff file and see what might be causing trouble?
 
Thank you very mcuh
 
Ashley Lu
Research Associate
 
<image003.jpg>
 
+6421921186
[hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited
 
Postal Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Private Bag 4704, , Christchurch, 8140, New Zealand
Physical Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Gerald Street, Lincoln, 7608, New Zealand
 
The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
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 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.
<test2.gff>------------------------------------------------------------------------------
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Re: webGbrowse

Ram Podicheti-2
Actually, you may want to define all the three contigs you are using in your GFF file in the same way. -Ram


On May 15, 2012, at 9:56 PM, Podicheti, Ram wrote:

Hi Ashley,
Can you try updating the first line of your GFF file setting the ID and Name of the contig to the sequence ID?

For eg: 

C01_001 Genbank contig 1 4659 . + 1 ID=C01_001;Dbxref=taxon:1095103;Name=C01_001;

ID and Name define the SeqID which identifies the landmark you are trying to display.

Please let me know how it goes.

Cheers,

Ram


On May 15, 2012, at 9:35 PM, Ashley Lu wrote:

Hi everyone,
 
I am completely new to GBrowse, and trying tying  to get my head around this toll.
So I have a genbank file, and I used the bp_genbank2gff3.pl to convert it to a gff format.
and I have trouble displaying this gff file on webGBrowse.
 
I’ve use the ‘gff3-validator’ tool to check the format of the gff file, and nothing unusual.
Also I’ve noticed that when I tried to do a search using column 1 of the gff file, sometimes it appears as ‘landmark name not recognised’,
and sometimes it did manage to find the landmark by giving a message ‘The following 3 regions match your request’,  but either ways, no image is produced.
 
Can you please have a look at this gff file and see what might be causing trouble?
 
Thank you very mcuh
 
Ashley Lu
Research Associate
 
<image003.jpg>
 
+6421921186
[hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited
 
Postal Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Private Bag 4704, , Christchurch, 8140, New Zealand
Physical Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Gerald Street, Lincoln, 7608, New Zealand
 
The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.
<test2.gff>------------------------------------------------------------------------------
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
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Re: webGbrowse

Ram Podicheti-2
<base href="x-msg://124/">
You can save each individual contig to a separate GFF file and load it into WebGBrowse. Even GBrowse will let you visualize one reference sequence at a time. Make sure you download the configuration file from the first contig instance which you can reupload to the subsequent contigs and that way you don't have to redo all the configuration steps. 
Thanks,

Ram


On May 16, 2012, at 12:28 AM, Ashley Lu wrote:

HI Ram,
Thank you very much for your reply!!!!
I was about to write to you…
And yes you could be perfectly correct, it did work with one conting(I deleted contig_00002 and contig_00003).
But not when there are more than one.
 
Ashley Lu
From: Podicheti, Ram [mailto:[hidden email]] 
Sent: Wednesday, 16 May 2012 4:26 p.m.
To: Ashley Lu
Subject: Re: [Gmod-webgbrowse] webGbrowse
 
Ashley,
I am not able to reproduce the error that you got and I do not see any issues with your GFF content either. However, there is one limitation of WebGBrowse. It cannot handle more than one SeqID in a GFF file and yours has three. I will try to use only one seqID per file. Let me play around with your file a little and get back to you.
Thanks,
 
Ram
 
 
On May 15, 2012, at 11:24 PM, Ashley Lu wrote:


Hi Ram,
 
Thank you very much for replying!!
Yes, I’ve changed the contigs names as you suggested and now it does make sense after reading through the tutorials.
But now the webGrowse is throwing exception, which I am quite confused, as I check the gff file by loading  it into mysql manually on my local machine using bp_seqfeature_load.pl.
Could it be the parent-child order not correctly listed in column 9???
An internal error has occurred
Could not open database.
------------- EXCEPTION -------------
MSG: IYO_00005
doesn't have a primary id
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:686
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:665
STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:319
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:325
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:222
STACK Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/memory.pm:166
STACK Bio::DB::SeqFeature::Store::new /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store.pm:376
STACK (eval) /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/Util.pm:187
STACK Bio::Graphics::Browser::Util::open_database /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/Util.pm:187
STACK toplevel /research/projects/webgbrowse/prod/v01/cgi-bin/gbrowse:180
-------------------------------------
 
 
 
Ashley Lu
Research Associate
 
+6421921186
[hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited
 
Postal Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Private Bag 4704, , Christchurch, 8140, New Zealand
Physical Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Gerald Street, Lincoln, 7608, New Zealand
 
From: Podicheti, Ram [mailto:[hidden email]] 
Sent: Wednesday, 16 May 2012 1:59 p.m.
To: Podicheti, Ram
Cc: Ashley Lu; [hidden email]
Subject: Re: [Gmod-webgbrowse] webGbrowse
 
Actually, you may want to define all the three contigs you are using in your GFF file in the same way. -Ram
 
 
On May 15, 2012, at 9:56 PM, Podicheti, Ram wrote:



Hi Ashley,
Can you try updating the first line of your GFF file setting the ID and Name of the contig to the sequence ID?
 
For eg: 
 
C01_001 Genbank
contig 1
4659 .
+ 1
ID=C01_001;Dbxref=taxon:1095103;Name=C01_001;
 
ID and Name define the SeqID which identifies the landmark you are trying to display.
 
Please let me know how it goes.
 
Cheers,
 
Ram
 
 
On May 15, 2012, at 9:35 PM, Ashley Lu wrote:



Hi everyone,
 
I am completely new to GBrowse, and trying tying  to get my head around this toll.
So I have a genbank file, and I used the bp_genbank2gff3.pl to convert it to a gff format.
and I have trouble displaying this gff file on webGBrowse.
 
I’ve use the ‘gff3-validator’ tool to check the format of the gff file, and nothing unusual.
Also I’ve noticed that when I tried to do a search using column 1 of the gff file, sometimes it appears as ‘landmark name not recognised’,
and sometimes it did manage to find the landmark by giving a message ‘The following 3 regions match your request’,  but either ways, no image is produced.
 
Can you please have a look at this gff file and see what might be causing trouble?
 
Thank you very mcuh
 
Ashley Lu
Research Associate
 
<image003.jpg>
 
+6421921186
[hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited
 
Postal Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Private Bag 4704, , Christchurch, 8140, New Zealand
Physical Address: Plant & Food Research Lincoln
Plant & Food Research Lincoln, Gerald Street, Lincoln, 7608, New Zealand
 
The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.
<test2.gff>------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions 
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<test1.gff>
 
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 If you are not the intended recipient you must not use, disseminate, distribute or
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