MATLAB: Do I receive errors when using the GETGENBANK function to access NCBI entries with multiple references in the Bioinformatics Toolbox 3.4 (R2009b)

Bioinformatics Toolbox

When I try to download nucleotide information from the NCBI database, I receive errors. For example, if I try to download information given accession number "NZ_ACIR00000000":
seq = getgenbank('NZ_ACIR00000000', 'SequenceOnly', 'true');
 I receive the following error:
 ??? Error using ==> getncbidata>accession2gi at 370
 The key NZ_ACIR00000000 has more than one sequence file associated with
 it in the nucleotide database.
 Error in ==> getncbidata at 179
 [giID,db] = accession2gi(accessnum,db,'quick');
 Error in ==> getgenbank at 82
     gb =
     getncbidata(accessnum,varargin{:},'database','nucleotide','fileformat','FASTA');

Best Answer

These errors stem from the fact that this NCBI entry is composed of several references or contigs. The ability to download NCBI download ncbi entries that are composed from several references or contigs is not available in the Bioinformatics Toolbox 3.4 (R2009b).
To work around it, access the ncbi web site manually and find out the list of individual entries that need to be downloaded, for example,
getgenbank('NZ_ACIR01000215')
getgenbank('NZ_ACIR01000216')
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