Entering edit mode
3.8 years ago
biostars_23e2e
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0
How to get related proteins and gene data of an organism (for eg. Lactobacillus ) preferably from NCBI.
I've tried e-utilities api and i am getting only fasta file for the proteins after running "fetch api" but what i am seeking is to get the detailed info about the genes and proteins(with pdb file) related to a given organism.
Thanks
This is not a
Toolpost - those are reserved for announcements of new tools. I have edited this time but please bear in mind for the future.yes, i didn't find anything else then ths selection close to what i was asking for. :)
It is just a
Question, which is the default.It sounds like you want a single command to download everything known about a set of proteins? No such system exists.
NCBI does not host crystallographic data, so you cannot get a PDB from NCBI. You may be able to do some database cross-referencing if the gene annotations include the structural information but that would be for a small minority of genes, if any.
You will have to aggregate information from multiple sources. Remember also that most proteins do not have validated annotations, much less actual structural information.
I tried the accession number from ncbi but that is not working in pdb database so i was wondering if, how can i use the accession number to get a pdb file.
Not easily no. These are separate databases which use different identifiers. If protein sequences and structures are what interest you, you can extract these from PDB directly - no need to involve NCBI.
PDB will allow you to filter by organism/genus etc, but there is no way to guarantee all the proteins come from one specific (e.g.) lactobacillus genome, and its very unlikely that they would.