From Gene To Genome From Kegg To Ncbi

Question

[Jjkoehorst]

As Kegg has better annotated datav I was wondering, I can extract genes from Kegg but is it possible to obtain the genome that belongs to that organism in kegg from ncbi.

Thus in short:

Kegg -> Certain genes NCBI -> Its corresponding genome (or actually the nucleotide sequence of all the genes)

[Pierre Lindenbaum]

Can you give use an example of KEGG identifier please ?

Answer 1

[Dmchurch]

There is not really a 'Kegg->Gene' file that I could find, but you can do the following query to get the information: Starting in BioSystems: http://www.ncbi.nlm.nih.gov/biosystems Do the following query in the search bar at the top of the page:

kegg[sourcename]

Note: you don't have to perform this query interactively, you can use E-utils (http://www.ncbi.nlm.nih.gov/books/NBK25501/)

When you get your results, you can look up the BioSystems ID to Gene ID relationship in this file: ftp://ftp.ncbi.nih.gov/pub/biosystems/CURRENT/biosystems_gene.*.gz

Data about the corresponding gene can be found at the Entrez Gene site (or on their FTP site, or using e-utils) http://www.ncbi.nlm.nih.gov/gene

Hope that helps!

[Larry_Parnell]

Nice answer! And welcome to BioStar - nice to have (another) voice from NCBI.

[Dmchurch]

thanks! glad it helped. I'm sure I'll be inconsistent in paying attention, but I'll try to be here when I can- largely because I learn a bunch by thinking about these questions!