Find Location Of Refseqgene Entry?

Question

[amillsx]

Hi,

UCSC RefGene seems to be great about mapping RNA and mRNA sequences to genomic coordinates (e.g. NR_046018.2 and NM_001005484.1), however I can't seem to figure out how to programmatically map RefSeqGene sequences to genomic coordinates. NG_011717.1 is one example ( http://www.ncbi.nlm.nih.gov/nuccore/NG_011717.1 ). It isn't in the RefGene database, and I can't find another resource that will map it. Does anyone have any idea?

Thanks!

Answer 1

[Pierre Lindenbaum]

using the NCBI data: chr12:9218304- 9273558

$ curl -s "ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/GCF_000001405.25_refseqgene_alignments.gff3" | \
grep  NG_011717

NC_000012.11    RefSeq    match    9218304     9273558    55252    +    .    ID=1;Target=NG_011717.1 1 55255 -;e_value=0;bit_score=102829;num_ident=55254;pct_identity_gap=99.9982;num_mismatch=1;pct_identity_ungap=99.9982;gap_count=0;pct_coverage=100;pct_identity_gapopen_only=99.998

[amillsx]

Awesome thanks so much! I'm a big fan of your question answering skills!