MatLab bioinformatics toolbox problem - (Jan/28/2007 )

When I use MatLab bioinformatics toolbox to search a sequence ,it ia always errors. why ?
the error as below:
Warning: Unable to get GenBank information for access number DQ366908. Trying FASTA...
> In getgenbank at 73
??? Error using ==> bioinfo\private\getncbidata
Can not interpret NCBI url data.
Who can tell me why it is like this?

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Well, and I am guessing here, but maybe it's because matlab can't read the format of that file. --- 'Can not interpret NCBI url data'. Are you sure you are using it correctly?

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I am sure that the command was no problem.
And i also use demo . the same results that can't interprete the url site

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Can you paste the code you write?
I use the Matlab Bioinformatics toolkit aswell.

What version of the toolkit are you using? Maybe your code is good but the software might have a bug?
from what I know, downloading a nucleotide seq from NCBI is

genbank('Accession number', 'SequenceOnly', true)

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Hi,
I have the same problem. If you managed to solve this error, plz tell me how.
thx

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Hi,
This error is a result of a change to the format of the URLs returned by the NCBI when searching for a record. A new version of the file used to connect to the NCBI's databases is now available.

Here are the required steps to download a revised version of an M-file that fixes the problem:

1. Quit MATLAB

2. Rename the following M-file:

$MATLAB\toolbox\bioinfo\bioinfo\private\getncbidata.m

(where $MATLAB = the MATLAB root directory on your machine)

Rename the file to getncbidata.m.old

3. Download the following file from our Web site:

http://www.mathworks.com/support/solutions...R/getncbidata.m

and place it in the same directory mentioned in step 2.

4. Restart MATLAB

5. After restarting MATLAB, issue the following command at the MATLAB prompt:

rehash toolboxcache

i found this solution while searching in the mathworks support for bioinformatics toolbox (try it and there will be no error )

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are Matlab and those toolboxes available in free versions?

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Hey guys,

I know this is an old thread, but I got the new version of Matlab (2007a) and I also get the same error message. The error in my case is with regards to line 182 (rather than line 73 as written in other posts above).

I'm confident the error is not my PC/internet connection because Matlab was the first application I installed after reformatting my PC this morning. I however think the problem is with regards to NCBI and possibly the fact that the HTTP urls are altered????
I don't know how many of us have tried this, but I was able to download GEO datasets perfectly fine; but not NCBI DNA or protein sequences. I'm starting to belive that this 'Cannot interpret URL' message has something to do with NCBI and not the MATLAB code.

Also, with regards to the update 'bio_info' kindly posted: This update is only applied to Matlab versions prior to Release 14 SP2. I downloaded such an update for my 2007A version and I still didn't get it to work.

If anyone here has had Matlab to work, I'd be appreciative of such assistance.
Thanks.

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