Question: How to obtain an annotation for the list of NCBI's Gene ID?
0
gravatar for rimgubaev
8 months ago by
rimgubaev180
Russia/Moscow/Skoltech
rimgubaev180 wrote:

I wonder if someone could help to find annotation for the list of NCBI's Gene ID. I got the Gene IDs in numeric format and I want to submit the list containing IDs of interest and retrieve the annotation for this IDs from NCBI as well as references to other databases like KEGG or UniProt.

geneid annotation ncbi • 241 views
ADD COMMENTlink written 8 months ago by rimgubaev180

Post examples when you ask this sort of a question. Numeric ID's could be/mean anything so it helps to be specific.

ADD REPLYlink written 8 months ago by genomax89k

I may not have completely understood your question, but you might want to try NCBI API (https://www.ncbi.nlm.nih.gov/books/NBK25501/) also biopython (http://biopython.org/DIST/docs/tutorial/Tutorial.html)

What would be more relevant to you is this snippet that I took from section 5.3.2 of BioPython tutorial (same link as above):

Now let’s use a handle to download a SwissProt file from ExPASy, something covered in more depth in Chapter 10. As mentioned above, when you expect the handle to contain one and only one record, use the Bio.SeqIO.read() function:

from Bio import ExPASy
from Bio import SeqIO

with ExPASy.get_sprot_raw("O23729") as handle:
    seq_record = SeqIO.read(handle, "swiss")
printseq_record.id)
printseq_record.name)
print(seq_record.description)
print(repr(seq_record.seq))
print("Length %i" % len(seq_record))
print(seq_record.annotations["keywords"])

Assuming your network connection is OK, you should get back:

O23729 CHS3_BROFI RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Full=Naringenin-chalcone synthase 3; Seq('MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDYYFRITKSEHLTELK...GAE', ProteinAlphabet()) Length 394 ['Acyltransferase', 'Flavonoid biosynthesis', 'Transferase']

ADD REPLYlink modified 8 months ago • written 8 months ago by manaswwm130
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