[Seqinr-forum] querying genbank to get the sequence for an accession

[Coghlan, Avril]

Dear Colleagues,

 

I am just learning how to use SeqinR and it looks extremely useful.

 

I am trying to figure out how I can use SeqinR to query the genbank database to get the sequence corresponding to a particular accession number, but am having a problem.

 

For example, the accession number corresponding to the Bacteriophage lambda genome is NC_001416.

I tried to get this sequence by typing in R:

 

Ø  library("seqinr")

 

Ø  choosebank("genbank")

 

 

Ø  query("lambda","AC=NC_001416")

 

The first two commands work fine, however, I get this error message from the query command:

   Error in query("lambda", "AC=NC_000907") : 

     invalid request:"unknown accession number at (^): \"AC

 

I am not sure what I am doing wrong, as other requests are working fine for me, eg. the command

 

Ø  query("lambda","AC=CP001252")

 

works fine for me.

 

Does anyone know what I am doing wrong?

I will be very grateful for any advice you can give.

 

Regards,

Avril 

 

Avril Coghlan

Department of Microbiology

University College Cork

Ireland

 

 

 

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