how to import gene fasta file from NCBI using matlab 2016a
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Priyanka Roy
on 28 Feb 2017
Commented: Paola Favaretto
on 1 Mar 2017
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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Accepted Answer
Paola Favaretto
on 28 Feb 2017
Are you sure it is a valid accession number? When I search the NCBI databases with the id you provided, I get 0 results.
More Answers (1)
Paola Favaretto
on 1 Mar 2017
Edited: Paola Favaretto
on 1 Mar 2017
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 ...'
4 Comments
Paola Favaretto
on 1 Mar 2017
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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