BLAST gbrowse integration

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Image:BLAST2gbrowse.png

feature
annotation which describes or gives meaning to a certain region within a sequence (e.g. exons in a transcript_region, UTRs of a mRNA_region...)
track
a set of features that is grouped and visualized together in one row of the genome browsers graphical output in the overview, region or details sections
reference sequence
(genomic) sequence that is visualized in the genome browser (E.g. chromosome, contig or scaffold). All features visible in the tracks must have a localization on a reference sequence.

Contents

Visualization of BLAST results in the cosmoss.org GenomeBrowser

Visualization of BLAST hits on reference sequences

Some of the BLAST databases on cosmoss.org are also available as reference sequence databases in the GenomeBrowser. To enable direct visualization of a BLAST hit against one of these sequences in the GenomeBrowser, we integrated the two systems.

When BLASTing vs e.g. the P.patens.V1.1_genome database, hit scaffolds will contain a direct link to visualize the BLAST hit as a gbrowse feature in a special track called Your cosmoss BLAST hits.

GenomeBrowser link button in the BLAST hit section

Image:BLAST_gbrowse_integration_hit_link.png

BLAST hit feature in the GenomeBrowser

Image:BLAST_gbrowse_integration_browser_tracks.png

At first, you'll find the BLAST track at the lower end of the Details panel. But you can alter its location like any other track in gbrowse, e.g. put it on top like on the snapshot above.

The hits are visualized as features in the overview, region and details panels of the GenomeBrowser. If you click on the BLAST feature, you'll be redirected back to the hits' alignment section.

The maximal range of a BLAST hit, is limited by the implementation. Currently the maximum range a BLAST hit may span is 100kbp. We might raise this limit in the future.

Save and modify the BLAST result mapping for later reuse

Image:BLAST_gbrowse_integration_tracks_save.png

In case you want to save the resulting mapping information for later use, or in case you want to adjust the color of the features etc., access the annotation in text format.

By clicking on the "Download" link in the "upload your annotation" section at the bottom of the gbrowse main window, you can access and store the underlying annotation: E.g:

[BLAST_hit]
 strand_arrow = 1
 bgcolor = green
 fgcolor = green
 description=1
 label=1
 section=details+overview+region
 connector=dashed
 key=Your cosmoss BLAST hits

 reference=scaffold_15
 BLAST_hit	Phypa1_1_116123_on_scaffold_15 2610269-2610739,2671516-2671046 "jgi|Phypa1_1|116123|e_gw1.15.427.1" https://www.cosmoss.org/bm/tmp/my_querycFqkowP7SwBzPGl/Phypa1_1_116123.content#scaffold_15

 reference=scaffold_308
 BLAST_hit	Phypa1_1_116123_on_scaffold_308 493480-493010,500207-500677,512327-511857 "jgi|Phypa1_1|116123|e_gw1.15.427.1" https://www.cosmoss.org/bm/tmp/my_querycFqkowP7SwBzPGl/Phypa1_1_116123.content#scaffold_308

 ...

By altering the annotation and uploading it as custom annotation you can influence how the features are visualized. See the documentation or the workshop hands-on for details.

Finding hit sequences that are mapped in the GenomeBrowser

In addition to BLASTing directly against a genomic sequence, you might want to search against one of our transcript or protein databases. Some of these databases also have been mapped against the genome and are available in one of the tracks of the GenomeBrowser.

If you BLAST against one of these databases, the hit section will also contain a GenomeBrowser link button:

GenomeBrowser link button for finding mapped sequences

Image:BLAST_gbrowse_integration_search.png

Feature of the hit sequence is highlighted

Image:BLAST_gbrowse_integration_found.png

If the sequence can be mapped multiple times, you'll have to select your region of interest from the gbrowse search result list.

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