# Similar Genome Finder Service ## Overview The bacterial Similar Genome Finder Service will find similar public genomes in BV-BRC or compute genome distance estimation using [Mash/MinHash](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915045/). It returns a set of genomes matching the specified similarity criteria. ## See also * [Similar Genome Finder Service](https://bv-brc.org/app/GenomeDistance) * [Similar Genome Finder Service Tutorial](/tutorial/similar_genome_finder/similar_genome_finder) ## 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](../images/bv_services_menu.png) ![Similar Genome Finder Input Form](../images/similar_genome_finder_input_form.png) ## 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 BV-BRC 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 BV-BRC to use this option.* ## Advanced Options ### Parameters **Max Hits:** The maximum number of matching genomes to return. **P-Value Threshold:** Sets the maximum allowable p-value associated with the [Mash](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915045/) Jaccard estimate used in calculating the distance. **Distance:** Mash distance, which estimates the rate of sequence mutation under as simple evolutionary model using k-mers. The Distance parameter sets the maximum Mash distance to include in the Similar Genome Finder Service results. Mash distances are probabilistic estimates associated with p-values. **Scope:** Option for limiting the search to only Reference and Representative genomes, or all genomes in BV-BRC. ## Buttons **Search:** Launches the similar genome finder job. ## Output Results ![Similar Genome Finder Service Results](../images/similar_genome_finder_results.png) The Similar Genome Finder Service generates a table of matching genomes based on the options chosen. ### Action buttons After selecting one of the output files by clicking it, a set of options becomes available in the vertical green Action Bar on the right side of the table. These include * **Hide/Show:** Toggles (hides) the right-hand side Details Pane. * **Download:** Downloads the selected items (rows). * **Copy:** Copies the selected items to the clipboard. * **Group:** Opens a pop-up window to enable adding the selected sequences to an existing or new group in the private workspace. * **Genome:** Loads the Genome View Overview page corresponding to the selected feature. *Available only if a single feature is selected.* * **Genomes:** Loads the Genomes Table, listing the genomes that correspond to the selected features. *Available only if multiple features are selected.* More details are available in the [Action Bar](/quick_references/action_bar) Quick Reference Guide. ## References 1. Ondov BD, Treangen TJ, Melsted P et al. Mash: fast genome and metagenome distance estimation using MinHash, Genome biology 2016;17:132.