david ID conversion

Question

[hana]

Hello, I am trying to use david gene ID conversion tool. I have a list of locus tag and would like to convert them to ENTREZ gene ID. however in my gff3 file that I have downloaded from ncbi there are two different locus IDs. one is name locus tag with IDs like this : H0N27_RS00020 and the other one is named old locus tag with IDs like: H0N27_00020. in the old version there are no RS after _ I have tried both of them separately as input in david upload list and it does not recognize them. does anyone have any suggestions for me?

Answer 1

[GenoMax]

Looks like this is Aceinetobacter baumanii genome.

Using EntrezDirect:

$ esearch -db nuccore -query "H0N27_00020 [locus]" | elink -target gene | esummary | xtract -pattern DocumentSummary -element Id,Name,Description
66398801        F3P16_RS17620   OprD family outer membrane porin
66398254        F3P16_RS14840   trehalose-6-phosphate synthase
66395588        ompR    two-component system response regulator OmpR
66396900        adeN    multidrug efflux transcriptional repressor AdeN
66398414        trxA    thioredoxin
66395838        F3P16_RS02525   diguanylate cyclase
66395764        rpsD    30S ribosomal protein S4
66397833        csrA    carbon storage regulator CsrA
66396031        F3P16_RS03495   DNA-binding response regulator PmrA
66398265        ccsA    cytochrome c biogenesis protein CcsA