Genomic Context Analysis

Question

[Thais]

Hi everyone!

This is my first time doing genomic context analysis, and I’m having a hard time with it.

I am currently looking for help in finding the neighboring genes for several bacterial proteins. But the only information I have is the protein's accession numbers from NCBI. Unfortunately, I noticed that the Genome Data Viewer on NCBI only includes some organisms, which limits my options.

Could anyone guide me on how to do this? Any tips or tools you recommend would be greatly appreciated!

Thank you very much in advance for your assistance!

[GenoMax]

Can you provide a couple of example accessions? It is possible that the protein accession numbers may be different than those assigned to that protein in a whole genome. You would need to look at the whole genome to get context.

Here is one example.

Say you are looking for dnaK in S. coelicolor A3 genome then

1. you could find the genome page by visiting https://ncbi.nlm.nih.gov/datasets/genome/ and search for the organism.
2. Once you reach the genome page, select the assembly that you are interested in https://ncbi.nlm.nih.gov/datasets/genome/?taxon=100226 from using https://ncbi.nlm.nih.gov/datasets/genome/GCF_008931305.1/.
3. On assembly page click on View annotated genes button to get to https://ncbi.nlm.nih.gov/datasets/gene/GCF_008931305.1/.
4. Once there search for specific gene by clicking on Filters and then searching with name in Search by name or symbol box --> https://ncbi.nlm.nih.gov/datasets/gene/GCF_008931305.1/?search=dnaK.
5. This will show you the gene and more importantly the genomic location which is NZ_CP042324.1:4050872-4052728 in this case.
6. Now you can go back to the filters box and this time search with an expanded region NZ_CP042324.1:4049872-4058728 using genomic locations box and that will show you a list of genes in this regions in table.

Answer 1

[Brian Bushnell]

Have you tried using a viewer like IGV? It lets you load a specific genome, plus tracks that show gene locations. All you need to do is download IGV, the genome, and a gff file showing where the genes are.