Connecting to databases: exercise part 1

Check your learning: connecting to databases

In this activity we will download and search the NCBI database list to find the blaKPC gene. You can find out more about this gene in this review article.

Step 1: Navigate to the NCBI database FTP page and download the database overview file

• You can access the full database by going to https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ in your browser.

This will bring up a list of different files, each with a different purpose. The one we care about is the ReferenceGeneCatalog.txt file.

• Right click that file and save it to your computer. If having trouble, you can download it from the bottom of this step.
• This file is a TSV (tab separated values) file. You should be able to load this directly into excel or similar to make search and filtering easier

If you are having issues with that, I have created an excel version of this file for you which you can download it from the bottom of this step.

• The database overview is made up of many columns, each with different information about the AMR-related genes and alleles which are in the rows.
• The database overview file has many columns but the ones we care about are:

Gene_family: the name of the gene that relates to that row entry

Product_name: What protein is created by that gene

Class: the general type of antimicrobial that this gene causes resistance to

Subclass: the specific type of antimicrobial that this gene causes resistance to

Pubmed_reference: the publication that is the underlying evidence for this genotype-phenotype link

Db_vesion: What is the version of the NCBI website you are looking at (important when writing your methods section)

• Ensure you are familiar with the different columns

• Use either the search function in excel or the filter function to find in the column gene_family the gene blaKPC

All allele entries for this gene should be together in the file so ensure you are looking at the different rows, not just the first one for this gene.

• In the next step you can answer the questions about this gene, so when you are ready, click Next button.