Tutorial: Proteome Comparison Service

Overview

This set of short videos provides a step-by-step demonstration of using the PATRIC Proteome Comparison Service to identify insertions and deletions in up to nine target genomes that are compared with one reference, which can be a researcher’s private genome in PATRIC, a genome that has been annotated outside PATRIC, any of the publicly available genomes in PATRIC, or a set of proteins that you have saved in PATRIC as a feature group.

1. Selecting parameters (8:13)

2. Selecting a reference genome (3:05)

3. Using a feature group or FASTA file as input (5:20)

4. Using a FASTA file as the reference (3:38)

5. Using a feature group as the reference (2:04)

6. Selecting the genomes to use for the comparison (5:57)

7. 3 flavors of reference genomes (5:38)

8. Reviewing the output job results (22:54)

9. Citing PATRIC and getting help (5:52)

See also

• Proteome Comparison Service

• Proteome Comparison Service Tutorial (document)

Using the Proteome Comparison 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. Selecting parameters (8:13)

2. Selecting a reference genome (3:05)

3. Using a feature group or FASTA file as input (5:20)

4. Using a FASTA file as the reference (3:38)

5. Using a feature group as the reference (2:04)

6. Selecting the genomes to use for the comparison (5:57)

7. 3 flavors of reference genomes (5:38)

8. Reviewing the output job results (22:54)

9. Citing PATRIC and getting help (5:52)

References

• Overbeek, R., et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic acids research, 2014. 42(D1): p. D206-D214.