Getting DNA sequences by ncbi eutils for a specific assembly e.g.: hg19, hg38, GRCh37.p13 or GRCh38.p6?
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4.8 years ago
burcakotlu ▴ 40

Dear all,

Is there a way to get DNA sequences for a specific assembly (for a given chromosome, start and end coordinates) using ncbi eutils?

String eFetchString = "https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=" + refSeqId + "&strand=1" + "&seq_start=" + oneBasedStart + "&seq_stop=" + oneBasedEnd + "&rettype=fasta&retmode=text";

My code above get DNA sequences in GRCh38.p6, I guess. (latest assembly right now.) Is there a way to specify the assembly and get DNA sequences in GRCh37.p13 or hg19 using ncbi eutils?

By the way, right now I'm focused on ncbi based solutions since I have coded in that way up to now. But I definitely would like to hear about other ways of doing this for my further studies.

Thanks in advance, Bur├žak Otlu

ncbi eutils efetch dna sequences • 1.3k views
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