Similar Genome Finder Service

Overview

The Similar Genome Finder Service will find similar public genomes in PATRIC or compute genome distance estimation using Mash/MinHash. It returns a set of genomes matching the specified similarity criteria.

Using the Similar Genome Finder Service

The Similar Genome Finder submenu option under the Services main menu (Genomics category) opens the Similar Genome Finder input form (shown below).

Similar Genome Finder Menu

Similar Genome Finder Input Form

Select a Genome

Specifies the genome to use as the basis for finding other similar genomes

Search by Genome Name or Genome ID

Selection box for specifying genome in PATRIC to use as the basis of comparison

Or Upload FASTA

Alternate option for uploading a FASTA file to use as the basis of comparison. Note: You must be logged into PATRIC to use this option.

Advanced Options

Parameters

Max Hits: The maximum number of matching genomes to return.

P-Value Threshold: Cutoff threshold for p-value.

Distance: Mash distance, which estimates the rate of sequence mutation under as simple evolutionary model using k-mers.

Scope: Option for limiting the search to only Reference and Representative genomes, or all genomes in PATRIC.

Buttons

Search: Launches the similar genome finder job.