Check how many entries in Genbank have a 'rep_origin' feature
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21 months ago
Zoya • 0

I am trying to figure out how many bacteria in Genbank have their origin of replication annotation with 'rep_origin'. Is there any way to easily check how many entries have this feature?

Thanks!

annotation feature rep_origin Genbank • 528 views
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Entering edit mode
21 months ago
GenoMax 139k

Following may be inaccurate so take it for what it is. Using EntrezDirect:

$ esearch -db nuccore -query "rep_origin [F_KEY]"
<ENTREZ_DIRECT>
  <Db>nuccore</Db>
  <WebEnv>MCID_62a226627e333e74ae2610c0</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>**45589**</Count>
  <Step>1</Step>

Limiting to just bacteria

$ esearch -db nuccore -query "rep_origin [FEATURE] AND 2 [taxID]"
<ENTREZ_DIRECT>
  <Db>nuccore</Db>
  <WebEnv>MCID_62a226dd6a789f35f21aa4ec</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>**11009**</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>
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Thank you so much much! I'm getting the same results. Is it possible to download the accessions for all entries matching my query? I assume there is, but this is my first time using EntrezDirect.

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