Question: How To Properly Limit Result From Eutils To Get Tinyseq Xml Output
1
gravatar for user56
7.0 years ago by
user56290
United States
user56290 wrote:

I have a gene of interest. Eg., TPMP It is this one: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=7172

In XML I can get the same info via this link: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=7172&retmode=xml

I can see that the reference sequence has accession number NC_000006 in NUCORE. I need position seq_start=18128542&seq_stop=18155374

An nice web view of my problem is here: http://www.ncbi.nlm.nih.gov/nuccore/NC_000006.11?from=18128542&to=18155374&report=genbank&strand=true (*)

How can I convert the last link (marked by star) to get the same info in XML. My goal was to get TinySeq XML format back. I tried this, but with no good luck. I always get the full 6th chromosome http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_000006&strand=2&seq_start=18128542&seq_stop=18155374&rettype=fasta&retmode=xml (warning, 160MB file)

eutils • 1.6k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 7.0 years ago by user56290

hum, I think it's a bug with the XML format because "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=224589818&strand=2&seq_start=18128542&seq_stop=18155374&rettype=fasta&retmode=text" works fine.

ADD REPLYlink written 7.0 years ago by Pierre Lindenbaum119k

Wow. Thanks for pointing that . I noticed that the IDs are strange. What is that second ID? Given this fact, now I just need to translate from NC_000006.11 to the different ID system (224589818). Any hits appreciated.

ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by user56290

it's the NCBI gi : http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html

ADD REPLYlink written 7.0 years ago by Pierre Lindenbaum119k
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