Getting Sequences Of A Given Chrnumber, Start And End Positions For Grch37/Hg19 Using Eutils In Java

Question

[burcakotlu]

Hi,

Is it possible to get sequences of a given chrNumber, start and end positions for GRCh37/hg19 using eutils in java?

Is there a way to indicate genome build and group label in efetch?

Thanks,

Burçak Otlu

[burcakotlu]

http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000001&seq_start=97533596&seq_stop=97533606&rettype=fasta&retmode=text

gives

gi|568815597:97533596-97533606 Homo sapiens chromosome 1, GRCh38 Primary Assembly ATCAAGGTGAG

which is for GRCh38 Primary Assembly

Answer 1

[Brad Chapman]

You want to reference the accession number for your chromosome suffixed with the version number for GRCh37, so use NC_000001.10:

$ wget -O /dev/stdout 'http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000001.10&seq_start=97533596&seq_stop=97533606&rettype=fasta&retmode=text'
gi|224589800:97533596-97533606 Homo sapiens chromosome 1, GRCh37.p13 Primary Assembly
AACCACCCAGT

Here are the RefSeq IDs for GRCh37:

http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/

[burcakotlu]

Many thanks, Burçak

Answer 2

[jimmy_zeng]

It's very easy to use the web API to reach your goal， instead of download the 3G hg19.fasta

getting sequence by A Given Chromosome, Start And End Positions For Grch37/Hg19

below is th examples :

http://genome.ucsc.edu/cgi-bin/das/hg38/dna?segment=chr17:7676091,7676196

http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr17:7676091,7676196