In the pioneering stages of my research on developing a multi-species multi-epitope UTI vaccine, I am encountering a significant challenge while exploring NCBI. For example, a search for E. coli yielded approximately 250,000 genomes, even after applying filters for completely annotated genomes, leaving around 200,000 genomes. Similar challenges were observed for Pseudomonas, Klebsiella, and Enterococci. Is there a specialized database or curated collection cataloging genomes associated with urinary tract infections for these organisms, or could anyone provide recommendations for efficiently identifying and isolating UTI-related strains from these extensive genomic datasets
Hi Anshika Billa
in NCBI (https://www.ncbi.nlm.nih.gov/geo/) just type "urinary tract infection" at top right of the page in the search field. you'll get enough datasets or profiles to dig and find exactly what needed.
all the best
fred
Hii Anshika,
Assuming you have miniconda installed on your system, follow these steps to create a separate environment for NCBI datasets, install the command-line tool, and proceed with data collection:
Step 1: Create a separate environment for NCBI datasets
conda create -n ncbi_datasets
conda activate ncbi_datasets
conda install -c conda-forge ncbi-datasets-cli"
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