Question: NCBI Gene(Nucleotide sequence) to chromosome location
1
gravatar for stanedav
2.7 years ago by
stanedav40
stanedav40 wrote:

Hello, recently I am working on my own pipeline in python. I am downloading page from NCBI Sequence viewer with defined ID (NM_000304.3) in this case:

https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=NM_000304.3&db=nuccore&retmode=html

On this page I am getting sequence of gene (last part of page ORIGIN) and also table of features. For next step I need to assign whole sequence to chromosome location, in this case it is this information: 17 NC_000017.10 (15133094..15168674, complement) from this page, which can be accessed from link in feature table in [1]:

https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=5376

Problem is, that if I download this page, I am getting page without data (its overwritten by javascript). I am looking for way, how to get information about chromosome location from [2] (Genetic context) or any other tool or webpage, which can helps me to convert nucleotide ID to chromosome location - it will be done for many genes in python code.

tl;dr: I want to convert Nucleotide ID (NM_00304.3) (or seqeunce) to chromosome location (chr 17 - 15133094:15168674), I prefer to use some web api through python code...

Thank for any suggestions

python gene genome ncbi • 1.1k views
ADD COMMENTlink modified 2.7 years ago by newbiebio80 • written 2.7 years ago by stanedav40
1

Have you looked at NCBI e-utils?

ADD REPLYlink written 2.7 years ago by genomax71k

Actually I tried to use e-utils previously and without success, now I worked more deeply and solved the problem. Thank you!

ADD REPLYlink written 2.7 years ago by stanedav40
1
gravatar for newbiebio
2.7 years ago by
newbiebio80
newbiebio80 wrote:

Maybe you can try UCSC MySQL. This is a tutorial http://crazyhottommy.blogspot.com/2013/11/mysql-rocks.html

Then type as bellow

select chrom, name,txStart,txEnd from refGene where name=''NMxxx";

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by newbiebio80
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