The new BLAST widget seamlessly integrates your results into NCBI’s Genome Data Viewer (GDV)


Want to analyze your BLAST results in the context of a genome browser? Want to compare those results against other genome assembly annotations? The BLAST widget, a new browser feature, lets you do that. It provides direct access within GDV to execute and manage BLAST queries (blastn, tblastn) aligned to the specific assembly displayed in GDV.

To learn about this tool, keep reading or watch this short introduction video. Further details are in GDV’s help documents.

It’s easy to get started. If you’ve run a successful BLAST search and your BLAST hit is an assembly sequence available in GDV, you’ll find a link to GDV that will let you view your BLAST results in GDV’s BLAST widget and render a BLAST track in the graphical view (Figure 1). If your BLAST hit is a protein [or transcript] annotated on the reference, the GDV link will take you to a graphical view of the corresponding assembly region.

fig.1 with inset

Figure 1. Links to Genome Data Viewer allow you to view your BLAST results in GDV’s BLAST widget and to render a BLAST track in the graphical view (as shown in Figure 2 and 3 respectively).

You can also launch the genome browser from the GDV home page. Open the BLAST menu in the left-side console and select the BLAST RID from your recent BLAST search (Figure 2). This menu automatically shows recent BLAST searches with results on the displayed assembly and lets you enter an active BLAST RID. The BLAST widget also lets you initiate new BLAST searches of the displayed assembly from within the GDV.

fig.2 with inset

Figure 2. Select BLAST RID menu. The menu is automatically populated with recent BLAST searches and allows you to enter an active RID.

Once loaded to the BLAST widget, the graphical display will update to show the corresponding alignment tracks at the top (Figure 3).

Fig.3

Figure 3. Highlighted alignment tracks. The track name is highlighted in yellow when the corresponding option is selected from the Tools menu.

The table within the BLAST widget summarizes alignment data for the selected search (Figure 4).

Fig.4

Figure 4. The table within the BLAST widget summarizes alignment data for the selected search.

To see details for all alignments located on the currently displayed assembly sequence, launch the BLAST Alignment Inspector (Figure 5) from within the BLAST widget.

Figure 5. Click on the icon (circled in red) to launch the BLAST inspector.

Figure 5. Click on the icon (circled in red) to launch the BLAST inspector.

We are interested to hear from you! Please send any feedback to  info@ncbi.nlm.nih.gov or use the “Support Center” link on any Genome Data Viewer page.

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