[Gmod-ajax] Question about blasting in JBrowse

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[Gmod-ajax] Question about blasting in JBrowse

Seyed Ahmad Mousavi
Hi Hans,

Sorry for bothrering you again; I will appreciate your precious helps.

I have working on JBrowse for my project during these weeks, and I faced with a basic problem.

My question is there any way to add Blast tool or similar other tools into JBrowse ? or I should use Blast outside Jbrowse?

Thanks for your helps.

Best regards,
Ahmad





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Re: Question about blasting in JBrowse

Raymond Wan-2
Hi Ahmad,


On Fri, Aug 26, 2016 at 1:58 PM, Seyed Ahmad Mousavi
<[hidden email]> wrote:
> My question is there any way to add Blast tool or similar other tools into
> JBrowse ? or I should use Blast outside Jbrowse?


You should apply Blast outside of JBrowse.

JBrowse is a genome browser and just displays aligned sequences on to
some backbone (i.e., chromosome).  The aligning of sequences should be
done separately by Blast or some other program.

Generally, both should work together as part of your workflow -- it
doesn't make sense to "add" Blast (or other similar tool) to within
JBrowse or vice-versa.

Ray

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Re: Question about blasting in JBrowse

Hans Vasquez-Gross
In reply to this post by Seyed Ahmad Mousavi
Hi Seyed,

Like Raymond suggest, I implement BLAST outside of JBrowse.  In the BLAST results page, I generate a link to JBrowse with the BLAST results encoded in the URL.   There is documentation in the JBrowse configuration guide, however, here is an example link that may help.

&loc=IWGSC_CSS_5BL_scaff_10869581%3A1..12858&tracks=DNA&highlight=IWGSC_CSS_5BL_scaff_10869581%3A1680..9155&addFeatures=%5B%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 8893%2C "end"%3A 9155%2C "name"%3A "MyBLASTHit_1"%2C "description" %3A "evalue 3e-116"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 1680%2C "end"%3A 1864%2C "name"%3A "MyBLASTHit_2"%2C "description" %3A "evalue 2e-80"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 8628%2C "end"%3A 8807%2C "name"%3A "MyBLASTHit_3"%2C "description" %3A "evalue 5e-76"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 6730%2C "end"%3A 6830%2C "name"%3A "MyBLASTHit_4"%2C "description" %3A "evalue 1e-38"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 5565%2C "end"%3A 5648%2C "name"%3A "MyBLASTHit_5"%2C "description" %3A "evalue 5e-31"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 6416%2C "end"%3A 6488%2C "name"%3A "MyBLASTHit_6"%2C "description" %3A "evalue 5e-25"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 7903%2C "end"%3A 7946%2C "name"%3A "MyBLASTHit_7"%2C "description" %3A "evalue 2e-10"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 8061%2C "end"%3A 8104%2C "name"%3A "MyBLASTHit_8"%2C "description" %3A "evalue 3e-09"%7D%5D&addTracks=%5B%7B"label"%3A"blast"%2C"store"%3A"url"%2C"type"%3A"JBrowse%2FView%2FTrack%2FHTMLFeatures"%2C "key"%3A"BlastHSP Results"%7D%5D%0A



BrokenDown into subsections:
Choose contig to display
&loc=IWGSC_CSS_5BL_scaff_10869581%3A1..12858

Choose tracks to load
&tracks=DNA%2Cblast

Highlight overall region of BLAST result
&highlight=IWGSC_CSS_5BL_scaff_10869581%3A1680..9155

Add the features hits to the 'blast' track
&addFeatures=%5B%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 8893%2C "end"%3A 9155%2C "name"%3A "MyBLASTHit_1"%2C "description" %3A "evalue 3e-116"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 1680%2C "end"%3A 1864%2C "name"%3A "MyBLASTHit_2"%2C "description" %3A "evalue 2e-80"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 8628%2C "end"%3A 8807%2C "name"%3A "MyBLASTHit_3"%2C "description" %3A "evalue 5e-76"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 6730%2C "end"%3A 6830%2C "name"%3A "MyBLASTHit_4"%2C "description" %3A "evalue 1e-38"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 5565%2C "end"%3A 5648%2C "name"%3A "MyBLASTHit_5"%2C "description" %3A "evalue 5e-31"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 6416%2C "end"%3A 6488%2C "name"%3A "MyBLASTHit_6"%2C "description" %3A "evalue 5e-25"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 7903%2C "end"%3A 7946%2C "name"%3A "MyBLASTHit_7"%2C "description" %3A "evalue 2e-10"%7D%2C%7B"seq_id"%3A"IWGSC_CSS_5BL_scaff_10869581"%2C "start"%3A 8061%2C "end"%3A 8104%2C "name"%3A "MyBLASTHit_8"%2C "description" %3A "evalue 3e-09"%7D%5D

Add the blast track
&addTracks=%5B%7B"label"%3A"blast"%2C"store"%3A"url"%2C"type"%3A"JBrowse%2FView%2FTrack%2FHTMLFeatures"%2C "key"%3A"BlastHSP Results"%7D%5D%0A

I hope this helps.

Cheers,
-Hans

On Thu, Aug 25, 2016 at 10:58 PM, Seyed Ahmad Mousavi <[hidden email]> wrote:
Hi Hans,

Sorry for bothrering you again; I will appreciate your precious helps.

I have working on JBrowse for my project during these weeks, and I faced with a basic problem.

My question is there any way to add Blast tool or similar other tools into JBrowse ? or I should use Blast outside Jbrowse?

Thanks for your helps.

Best regards,
Ahmad







--
Hans Vasquez-Gross
Graduate Student
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd

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