Proteome Comparison Service

Overview

The Proteome Comparison Service performs protein sequence-based genome comparison using bidirectional BLASTP. This service allows users to select up to eight genomes, either public or private, and compare them to a user-selected or supplied reference genome. The proteome comparison result is displayed as an interactive circular genome view and is downloadable as a print-quality image or tabular comparison results.

Using the Proteome Comparison Service

The Proteome Comparison submenu option under the Services main menu (Protein Tools category) opens the Proteome Comparison input form (shown below). Note: You must be logged into PATRIC to use this service.

Proteome Comparison Service Menu

Options

Proteome Comparison Service Input Form

Parameters

Advanced parameters:

Minimum % coverage: Minimum percent sequence coverage of query and subject in blast. Use up or down arrows to change the value. The default value is 30%.

BLAST E value: Maximum BLAST E value. The default value is 1e-5.

Minimum % Identity: Minimum percent sequence identity of query and subject in BLAST. Use up or down arrows to change the value. The default value is 10%.

Output Folder

The workspace folder where results will be placed.

Output Name

Name used to uniquely identify results.

Reference Genome Selection

Select a reference genome from the genome list or a FASTA file or a feature group. Only one reference is allowed.

Select a genome

Type or select a genome name from the genome list.

Or a FASTA file

Select or upload an external genome file in protein FASTA format.

Or a feature group

Select a feature group from the workspace to show comparison of specific proteins instead of all proteins in a genome.

Comparison Genomes Selection

Select up to total of 9 genomes from the genome list or FASTA files or a feature groups and use the plus buttons to place the genomes to the table .

Select genome

Type or select a genome name from the genome list.

And/or select FASTA file

Select or upload an external genome file in protein FASTA format.

And/or select feature group

Select a feature group from the workspace.

Buttons

Reset: Resets the input form to default values

Submit: Launches the proteome comparison job. Upon completion, the result is displayed as an interactive circular genome view and is downloadable as a print-quality image or tabular comparison results.