# Tutorial: Protein Family Sorter Service

## Overview
This set of short videos provides a step-by-step demonstration of using the PATRIC Protein Family Sorter to analyze protein families across a set of closely related bacterial genomes.

1. [Using Global Search (7:37)](#pfs1)
2. [Creating a genome group (5:01)](#pfs2)
3. [Submitting a Protein Family Sorter Service analysis job (5:44)](#pfs3)
4. [Protein Family Sorter tabular results (7:41)](#pfs4)
5. [Filtering tabular results (8:17)](#pfs5)
6. [Heatmap filtering (5:02)](#pfs6)
7. [Heatmap clustering (4:47)](#pfs7)
8. [Anchoring and downloading heatmap data (6:01)](#pfs8)
9. [Using the Feature Table and Compare Region Viewer (12:40)](#pfs9)
10. [Downloading sequences from Feature Table and viewing in the Genome Browser (9:38)](#pfs10)
11. [BLASTing a genomic region (10:21)](#pfs11)

### See also
* [Protein Family Sorter Service](https://patricbrc.org/app/ProteinFamily)
* [Comparing Protein Families Across Genomes Tutorial](https://docs.patricbrc.org//tutorial/protein_family_sorter/protein_family_sorter.html) (document)
* [Protein Families Tab User Guide](../organisms_taxon/protein_families.html)

## Using the Protein Family Sorter Service

Links to the videos are provided below.  They can also be viewed in order in the [PATRIC YouTube channel playlist](https://www.youtube.com/playlist?list=PLsstVALeacEKNYElzKV7YvSeG9JP0Jq0j). Relevant references are provided at the bottom of this page.

<a name="pfs1"></a>
##### 1. Using Global Search (7:37)
<iframe width="560" height="315" src="https://www.youtube.com/embed/B_sH3Lpx32I" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs2"></a>
##### 2. Creating a genome group (5:01)
<iframe width="560" height="315" src="https://www.youtube.com/embed/zqTtJqfDpzE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs3"></a>
##### 3. Submitting a Protein Family Sorter Service analysis job (5:44)
<iframe width="560" height="315" src="https://www.youtube.com/embed/Zcy4PfGjRE8" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs4"></a>
##### 4. Protein Family Sorter tabular results (7:41)
<iframe width="560" height="315" src="https://www.youtube.com/embed/qbi9No8wegs" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs5"></a>
##### 5. Filtering tabular results (8:17)
<iframe width="560" height="315" src="https://www.youtube.com/embed/jlPL7SJgLlU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs6"></a>
##### 6. Heatmap filtering (5:02)
<iframe width="560" height="315" src="https://www.youtube.com/embed/oVGI7nhcBaA" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs7"></a>
##### 7. Heatmap clustering (4:47)
<iframe width="560" height="315" src="https://www.youtube.com/embed/mZyWG3jSZVY" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs8"></a>
##### 8. Anchoring and downloading heatmap data (6:01)
<iframe width="560" height="315" src="https://www.youtube.com/embed/KMeI-JARQa0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs9"></a>
##### 9. Using the Feature Table and Compare Region Viewer (12:40)
<iframe width="560" height="315" src="https://www.youtube.com/embed/sF6CyRHPid0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs10"></a>
##### 10. Downloading sequences from Feature Table and viewing in the Genome Browser (9:38)
<iframe width="560" height="315" src="https://www.youtube.com/embed/8W72pw58nh4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="pfs11"></a>
##### 11. BLASTing a genomic region (10:21)
<iframe width="560" height="315" src="https://www.youtube.com/embed/NhnJ8zwNc5o" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## References
* Davis, J.J., et al., PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. Front Microbiol, 2016. 7: p. 118.
* Meyer, F., R. Overbeek, and A. Rodriguez, FIGfams: yet another set of protein families. Nucleic acids research, 2009. 37(20): p. 6643-6654.