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)
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Jjkoehorst •
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!
Nice answer! And welcome to BioStar - nice to have (another) voice from NCBI.
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!
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Can you give use an example of KEGG identifier please ?