TaxID to RefSeq

Question

[fyfes]

Hi, I have a NCBI tax ID and I would like to find a code that can translate it to RefSeq Id. Is that possible?

[GenoMax]

Post some examples. As posted I am not sure this question makes sense. A particular TaxID is going to have many sequences in RefSeq. Are you interested in just RefSeq genome?

[fyfes]

yes exactly, being given a tax ID 435590 i would like to find its RefSeq Id and download the genome

[fyfes]

Thank you a lot! It was very useful

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db taxonomy -query "435590  [taxID]" | elink -target nuccore | efetch -format docsum | xtract -pattern DocumentSummary -if SourceDb -contains refseq -element Caption,Title,SourceDb
NC_009614       Bacteroides vulgatus ATCC 8482, complete sequence       refseq
NR_074515       Bacteroides vulgatus ATCC 8482 16S ribosomal RNA, partial sequence      refseq
NR_075351       Bacteroides vulgatus ATCC 8482 strain ATCC 8482 5S ribosomal RNA, complete sequence     refseq

If you look in the assembly database you will get the download links:

$ esearch -db taxonomy -query "435590  [taxID]" | elink -target assembly | efetch -format docsum | xtract -pattern DocumentSummary -element RefSeq,Organism,RefSeq_category,FtpPath_RefSeq
GCF_900624655.1 Bacteroides vulgatus ATCC 8482 (CFB group bacteria)     na      ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/624/655/GCF_900624655.1_81B11
GCF_000012825.1 Bacteroides vulgatus ATCC 8482 (CFB group bacteria)     representative genome   ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/012/825/GCF_000012825.1_ASM1282v1