GView Server

GView Server is a comparative genomics server and front end to GView, a circular and linear genome viewer. It allows sequence information to be analyzed and the results visualized in an intuitive manner. A single reference genome (in GenBank, EMBL) can be uploaded and the appearance customized, or multiple genomes can be uploaded to perform comparative analysis. GView Server uses BLAST to compare the reference with any other genomes uploaded and contains a number of predefined BLAST analysis types for different use cases.

Step 1: Choose Analysis and Upload Reference

Choose the analysis type to perform and select a reference sequence file to upload. Accepted formats are GenBank and EMBL, and the file should contain a complete, nucleotide genome. If you would like to have your results e-mailed to you upon completion, enter your e-mail address below.

Analysis Type Select analysis type to see a description below
Select a sequence file Upload your reference genome (example)
E-mail A valid e-mail address (optional)

Display reference genome features

Upload a rich sequence file (GenBank or EMBL) to display features in an interactive GView map.
More info

Process:

Upload a reference genome
Customize output styles
View results

Example results:

A full map of the features of a reference genome

Zoomed in view of the features of a segment of a reference genome

Create a BLAST atlas

Create a BLAST atlas by uploading a reference genome and one or more related genomes. Regions will be displayed where there is similarity between the reference genome and one of the related genomes.
See more info

Process:

Upload a reference genome
Upload query sequence files for BLAST analysis
Set BLAST analysis options
Customize output styles
View results

Example results:

BLAST atlas containing a reference genome and 2 query genomes

Display the core regions of a genome

View the core regions of a genome by uploading a reference genome and a query file containing multiple related genomes. This will highlight the regions in the reference genome that also exist in all of the query genomes.
See more info

Process:

Upload a reference genome
Upload a query file containing multiple genomes that are closely related to the reference
Set BLAST analysis options
Customize output styles
View results

Example results:

Display the accessory regions of a genome

View the accessory regions of a genome by uploading a reference genome and a query file containing multiple related genomes. The resulting regions displayed will be those that had BLAST hits to some sequences in the query file, but not to every sequence in the query file.
See more info

Process:

Upload a reference genome
Upload a query file containing multiple genomes that are closely related to the reference
Set BLAST analysis options
Customize output styles
View results

Example results:

View of the accessory regions of a genome

Display the unique regions of a genome

View the unique regions of a genome by uploading a reference genome and a query file containing multiple related genomes. The resulting regions displayed will be those that had no BLAST hits to any sequence in the query file.
See more info

Process:

Upload a reference genome
Upload a query file containing multiple genomes that are closely related to the reference
Set BLAST analysis options
Customize output styles
View results

Example results:

Display the signature regions of a genome

Find the signature regions of a genome by uploading a reference genome and a set of inclusion and exclusion genomes. The inclusion genomes should be very similar to the reference genome. The exclusion genomes should be similar to the reference genome, but lacking signature characteristics. The resulting regions displayed will be those that are found in the inclusion genomes but not in the exclusion genomes.
See more info

Process:

Upload a reference genome
Upload a file containing multiple genomes that demonstrate the signature aspects of your reference genome (inclusion sequences). Upload another file containing genomes that are closely related to the reference genome, but do not demonstrate the signature aspects (exclusion sequences)
Set BLAST analysis options
Customize output styles
View results

Example results:

View of the signature regions of a genome

Zoomed in view of the signature regions of a genome

Create a pangenome of query sequences

Create a pangenome by uploading a collection of similar query genomes. A seed genome is selected and other query genomes are compared to the seed to locate the unique regions. The seed is incrementally built up with the unique features of the queries to become the pangenome. A BLAST atlas is created to display the presence or absence of features within the query genomes compared to the pangenome.
See more info

Process:

Upload query genomes and select one as the seed genome
Set BLAST analysis options
Customize output styles
View results

Example results:

View of a pangenome BLAST atlas of 3 genomes

Zoomed in view of the pangenome BLAST atlas

Perform a reciprocal BLAST between two genomes

Upload a reference sequence file and a query sequence file to perform a reciprocal BLAST and display features in an interactive GView map.
See more info

Process:

Upload a reference genome
Upload a query genome
Set BLAST analysis options
Customize output styles
View results

Example results:

View of a reciprocal BLAST between two genomes

Zoomed in view of a reciprocal BLAST between two genomes

Create a custom GView analysis

Create a fully customized GView analysis. You can combine various analysis types to create a unique GView image. You can also use BLAST-Logic to create a new analysis type customized for your needs.

Note: The custom analysis builder is for advanced users only. Users are required to have knowledge of BLAST parameters and sequence file features to build a valid analysis.
See more info

Process:

Upload a reference genome
Upload query files and select analysis types
Customize output styles
View results

Example job creation:

Most recently updated on September 9, 2020.

An online, interactive GView assistant.