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. From these videos you will learn how to do the following:

  • Use the global search and the genome groups to select a set of genomes for analysis

  • Initiate a Protein Family Sorter Service job

  • Use the Protein Family Sorter tabular and heatmap features to analyze the job results

  • Download heatmap data

  • Use other tools such as Compare Region Viewer, Genome Browser, and BLAST to further interpret the results

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. Relevant references are provided at the bottom of this page.

1. Using Global Search (7:37)

2. Creating a genome group (5:01)

3. Submitting a Protein Family Sorter Service analysis job (5:44)

4. Protein Family Sorter tabular results (7:41)

5. Filtering tabular results (8:17)

6. Heatmap filtering (5:02)

7. Heatmap clustering (4:47)

8. Anchoring and downloading heatmap data (6:01)

9. Using the Feature Table and Compare Region Viewer (12:40)

10. Downloading sequences from Feature Table and viewing in the Genome Browser (9:38)

11. BLASTing a genomic region (10:21)

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.