Download discontinued gene record from NCBI via E-utils
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4 weeks ago

Hello,

I am trying to download gene sequences from NCBI via e-utils like this:

esearch -db gene -q "1511[Taxonomy ID] AND (grdA OR grdB OR grdC)[Gene Name]" | elink -db gene -target nuccore | efetch -db nuccore -format gene_fasta > gene_file.fasta

After that I would apply some awk and grep commands on gene_file.fasta to filter out only needed sequences. Unfortunately, all matching records were discontinued. And even though esearch outputs 3 records, elink cannot create links to nucleotide database. Is there any way to download these discontinued records using e-utils?

Thank you in advance for any suggestion

E-utils NCBI Discondinued Gene • 230 views
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Entering edit mode
4 weeks ago
GenoMax 101k

I don't think you can do that.

$ efetch -db gene -id 647 -format fasta

1. BLYM
Official Symbol: BLYM and Name: avian lymphoma virus-derived transforming sequence [Homo sapiens (human)]
Chromosome: 1; Location: 1p32
This record was discontinued.
ID: 647

If you still wish to download the sequence anyway you could get it from the genome using the intervals below

$ esearch -db gene -q "1511[Taxonomy ID] AND (grdA OR grdB OR grdC)[Gene Name]" | esummary | xtract -pattern GenomicInfoType -element ChrAccVer,ChrStart,ChrStop
NC_014614.1 1264996 1265472
NC_014614.1 1266902 1268437
NC_014614.1 1265494 1266804
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Thank you it worked.

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