Examples

February 9, 2021: Job submission for GView Server is back to normal.

Examples

Presented here are examples of different analyses GView Server is capable of performing. Each example was generated by running the given input files through GView Server and keeping all other settings on the default values. A link to the results page for each example is given which provides access to launch the corresponding map in GView as well as download a table of the BLAST results.

  1. BLAST Atlas
  2. Pangenome Analysis
  3. Core Analysis
  4. Accessory Analysis
  5. Unique Analysis
  6. Signature Analysis
  7. Reciprocal Analysis
  8. Pangenome Phage Analysis

BLAST Atlas

Description

The BLAST Atlas example was created using a number of Listeria genomes from NCBI. The CDS regions in the reference genome were BLASTed against the CDS regions in the query genomes, and the top hits rendered in a genome map using GView. The inner-most slot on the map (orange) shows the CDS regions on the reference genome. The two outer slots (brown and red) show regions on the reference where there was a BLAST hit within one of the query files. Empty regions on the query slots (i.e. at approx. 700 kbp) indicate areas where there were no BLAST hits between the reference and the query files.

Files

Results

A results page containing the GView files and results table for this example can be viewed at blast atlas results.

Pangenome Analysis

Description

The Pangenome analysis example was created using three Listeria genomes. The inner-most slot (green) shows the constructed pangenome using all uploaded genomes. The pangenome is constructed by iteratively appending unique regions onto the initial seed genome, in this case 08-5578. The next slots show regions where there were BLAST hits between the constructed pangenome and the other uploaded genomes. The large gap between 3000 kbp and 0 kbp shows a region missing from the seed genome (08-5578) but found in one of the other genomes (hcc23). This region was appended onto the reference pangenome and is thus visible as a gap in the BLAST results for the seed genome slot (08-5578).

Files

Results

A results page containing the GView files and results table for this example can be viewed at pangenome results.

Core Analysis

Description

The Core Genome Analysis example was created using a number of Listeria genomes from NCBI. The CDS regions in the reference genome were BLASTed against the uploaded query sequences. The inner-most slot (brown) shows CDS regions on the reference, and the outer-most slot (red) represents the core genome. The core genome slot shows regions where a BLAST hit was present between the reference and all of the sequences in the query file.

Files

Results

A results page containing the GView files and results table for this example can be viewed at core results.

Accessory Analysis

Description

The Accessory Genome analysis example was created using a number of Listeria genomes from NCBI. The CDS regions in the reference genome were BLASTed against the uploaded query sequences. The inner-most slot (brown) shows all CDS regions on the reference. The outer-most slot (red) shows the accessory genome of the reference and query files. Only a region with a BLAST hit to one of the query genomes, but not all is displayed as the accessory genome. Regions which show up in the accessory genome are regions which are variable among the uploaded query genomes.

Files

Results

A results page containing the GView files and results table for this example can be viewed at accessory results.

Unique Analysis

Description

The Unique Genome analysis example was created using a number of Listeria genomes from NCBI. The reference genome was BLASTed against the uploaded query sequences. The inner-most slot (brown) shows all the CDS regions on the reference. The outer-most slot (red) shows the unique regions on the reference compared to the query sequences. The unique regions on the reference consist of those regions where there were no BLAST hits between the reference and query genomes.

Files

Results

A results page containing the GView files and results table for this example can be viewed at unique results.

Signature Analysis

Description

A Signature analysis example was created using a number of Listeria genomes. The inner-most slot (brown) shows the CDS regions on the reference. The outer-most slot (red) shows all CDS regions included in both 08-5578 (reference) and 08-5923 (inclusion), but not in hcc23 (exclusion). This was generated by doing a BLAST of 08-5578 (reference) CDS regions against both 08-5923 (inclusion) and hcc23 (exclusion) genomes, and filtering out hits to hcc23 from the final results.

Files

Results

A results page containing the GView files and results table for this example can be viewed at signature results.

Reciprocal Analysis

Description

The Reciprocal BLAST analysis example was created using a number of Listeria genomes from NCBI. The inner-most slot (brown) shows the CDS regions on the reference genome. The outer-most slot (red) shows the top hits of a reciprocal BLAST between the reference genome and query genome.

Files

Results

A results page containing the GView files and results table for this example can be viewed at reciprocal results.

Pangenome Phage Analysis

Description

In this example, previously identified phages were mapped onto a Listeria pangenome. The inner-most slot shows CDS regions from the constructed pangenome using all uploaded genome files. The following three slots (purple,light green,dark green) show BLAST hits from the pangenome to the three Listeria genomes. The outer-most three slots show BLAST hits from the pangenome to CDS regions of three complete phages.

Files

Results

A results page containing the GView files and results table for this example can be viewed at pangenome phage results.