how to import gene fasta file from NCBI using matlab 2016a

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Priyanka Roy
Priyanka Roy 2017-2-28
评论： Paola Favaretto 2017-3-1
I want to import gene fasta file from NCBI database using the Accession Number. I use the code Data = getgenbank('NP_752927.1'); but, getting this error : Error using getncbidata (line 191) The key NP_752927.1 was not found in the nucleotide database at this time. Please check that the input is a valid accession number or try again.
NOTE: This function is dependent on NCBI's Entrez tools and sequence databases. Changes to either may cause this function to break.
Error in getgenbank (line 70)
[varargout{1:nargout}] = getncbidata(accessnum,'fileformat','GenBank','database','nucleotide',varargin{:});
How will i resolve the error?

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采纳的回答

Paola Favaretto
Paola Favaretto 2017-2-28
Are you sure it is a valid accession number? When I search the NCBI databases with the id you provided, I get 0 results.
  1 个评论
Priyanka Roy
Priyanka Roy 2017-3-1
Escherichia coli O157:H7 str. Sakai, complete genome. NCBI Reference Sequence: NC_002695.1 ACCESSION NC_002695
I can manually download the Fasta file from NCBI database, but getting the same error while using the code : Data = getgenbank('NC_002695');
what will be the code for importing the fasta file directly from NCBI database ?

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更多回答（1 个）

Paola Favaretto
Paola Favaretto 2017-3-1
编辑：Paola Favaretto 2017-3-1
What version of Bioinformatics Toolbox are you using? I am able to download the sequence without issues.
You can get the sequence information by typing:
a = getgenbank('NC_002695', 'sequenceonly', true)
Or you can save the sequence in a FASTA formatted file by typing:
a = getgenbank('NC_002695', 'tofile', 'S:/myfile2.fa', 'fileformat', 'fasta')
This is a snippet of the output:
a =
struct with fields:
Header: 'NC_002695.1 Escherichia coli O157:H7 str. Sakai, complete genome'
Sequence: 'AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGC ...'
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Priyanka Roy
Priyanka Roy 2017-3-1
I run the code:
a = getgenbank('NC_002695', 'sequenceonly', true)
and then got this error:
Error using getncbidata (line 227) Cannot save the contents of the URL to 'C:\Users\Su\AppData\Local\Temp\tp1f17e28a_9c1a_40e3_a428_c56374602d85'.
Error in getgenbank (line 70) [varargout{1:nargout}] = getncbidata(accessnum,'fileformat','GenBank','database','nucleotide',varargin{:});
Paola Favaretto
Paola Favaretto 2017-3-1
See if this patch solves your problem. (NCBI switched their protocol to https in late September 2016).
If not, I suggest you contact MathWorks Customer Support to get the help you need to solve your particular problem.

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