What is the best way to get a set of all of the genes for a genome via entrez?
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9 months ago
DNAlias ▴ 10

What is the best way to get a set of all of the genes for a genome via entrez?

I tried using the term "GCF_009858895[AACC]" for the "gene" database, but got no hits.

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9 months ago
GenoMax 102k

Using Entrezdirect:

A. If you just need names

$ esearch -db assembly -query "GCF_009858895" | elink -target genome | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name,Description
ORF1ab  ORF1a polyprotein;ORF1ab polyprotein
S   surface glycoprotein
N   nucleocapsid phosphoprotein
ORF7a   ORF7a protein
ORF6    ORF6 protein
ORF3a   ORF3a protein
ORF7b   ORF7b
ORF10   ORF10 protein
M   membrane glycoprotein
E   envelope protein
ORF8    ORF8 protein

B. If you want additional information

$ esearch -db assembly -query "GCF_009858895" | elink -target genome | elink -target gene | efetch -format tabular
tax_id  Org_name    GeneID  CurrentID   Status  Symbol  Aliases description other_designations  map_location    chromosome  genomic_nucleotide_accession.versionstart_position_on_the_genomic_accession end_position_on_the_genomic_accession   orientation exon_count  OMIM
2697049 Severe acute respiratory syndrome coronavirus 2 43740578    0   live    ORF1ab  GU280_gp01  ORF1a polyprotein;ORF1ab polyprotein    ORF1a polyprotein;ORF1ab polyprotein            NC_045512.2 266 21555   plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740568    0   live    S   GU280_gp02, spike glycoprotein  surface glycoprotein    surface glycoprotein        NC_045512.2 21563   25384   plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740575    0   live    N   GU280_gp10  nucleocapsid phosphoprotein nucleocapsid phosphoprotein     NC_045512.2 28274   29533   plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740573    0   live    ORF7a   GU280_gp07  ORF7a protein   ORF7a protein           NC_045512.2 2739427759  plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740572    0   live    ORF6    GU280_gp06  ORF6 protein    ORF6 protein            NC_045512.2 2720227387  plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740569    0   live    ORF3a   GU280_gp03  ORF3a protein   ORF3a protein           NC_045512.2 2539326220  plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740574    0   live    ORF7b   GU280_gp08  ORF7b   ORF7b           NC_045512.2 27756   27887   plus0
2697049 Severe acute respiratory syndrome coronavirus 2 43740576    0   live    ORF10   GU280_gp11  ORF10 protein   ORF10 protein           NC_045512.2 2955829674  plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740571    0   live    M   GU280_gp05  membrane glycoprotein   membrane glycoprotein           NC_045512.2 26523   27191   plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740570    0   live    E   GU280_gp04  envelope protein    envelope protein            NC_045512.2 26245   26472   plus    0
2697049 Severe acute respiratory syndrome coronavirus 2 43740577    0   live    ORF8    GU280_gp09  ORF8 protein    ORF8 protein            NC_045512.2 2789428259  plus    0
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So does this mean that you are extracting the genes from the genome entry instead of the assembly entry? There are some assemblies that don't seem to have links to genomes.

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In this case the accession you provided is for an assembly. So linking it to a genome and then get the genes worked. If assemblies don't have genome links and/or have no annotation then you can't get the gene names for those.

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