MATLAB: How to extract qualifiers in a GBK file which are not parsed by “genbankread”

Bioinformatics Toolboxgbkgenbankreadregexp

The "genbankread" function does not parse all qualifiers in my GBK file.

For example, I include the "/label" qualifier for the "CDS" feature key, but a corresponding field does not appear in the "CDS" struct outputted by "genbankread".

Is it possible to parse this field into the "CDS" struct?

Best Answer

Unfortunately, the only GBK tags that are automatically parsed by "genbankread" are the ones that have a corresponding field in the outputted struct.

However, the full text of each feature is preserved in the "text" field.

You can use string/text functions, such as "regexp", to extract the desired fields from there.

As an example of how this may be done, please see the attached script that extracts the "/label" qualifier from each "CDS" feature in the attached file and adds a corresponding field (called "label") to the struct outputted by "genbankread".

Related Solutions

MATLAB: Were the ProbeSetNumber and ProbePairNumber columns removed from structs returned by AFFYREAD in MATLAB 7.5 (R2007b)

The AFFYREAD structure has been changed for the Bioinformatics Toolbox V3.0 - which is the toolbox release in conjunction with MATLAB 7.5 (R2007b).

The new GroupNumber column gives the same information as the ProbeSetNumber subfield did, except that the GroupNumber indexing is 1-based while the ProbeSetNumber was 0-based (in accordance with Affymetrix standards).

ProbePairNumber, however, was removed due to the perceived redundancy in the information it provided; the probe pair numbers are simply the row indices of the matrices contained in the ProbeSets field of the returned struct (each row represents the readings of one probe pair).

While the ProbePairNumber column was removed, it is possible to compute the probe pair numbers from the ProbeSets matrices, and if desired, insert them back into the returned struct. Shown below is code that would perform this:

for n = 1:length(affy_struct.ProbeSets)
      % Extract current ProbePair matrix
      CurPairs = affy_struct.ProbeSets(n).ProbePairs;
      % Generate indices
      CurPairNumbers = (1:length(CurPairs));
      % Force column vector
      CurPairNumbers = CurPairNumbers(:); 
      % ProbePairNumbers are inserted here
      CurPairs = [CurPairs(:,1) CurPairNumbers CurPairs(:,2:end)];
      % Reassign to ProbePairs
      affy_struct.ProbeSets(n).ProbePairs = CurPairs;
end

where affy_struct is the struct obtained by reading a CDF file with AFFYREAD.

You may also then insert 'ProbePairNumber' as one of the names in affy_struct.ProbeSetColumnNames by executing the following code:

CurNames = affy_struct.ProbeSetColumnNames;
CurNames = {CurNames{1} 'ProbePairNumber' CurNames{2:end}};
affy_struct.ProbeSetColumnNames = CurNames;

MATLAB: Am I unable to access the NCBI Entrez Database using GENBANKREAD in MATLAB 7.7 (R2008b)

Bioinformatics Toolbox does not have a function to read in GENE files directly. GENBANKREAD can only read in GENBANK files from the NUCLEOTIDE databases at NCBI

To work around this issue, use URLREAD to retrieve a file from the GENE database.

From the demo code example with GENBANKREAD replaced with URLREAD:

ch97struct = urlread([baseURL,'efetch.fcgi?',dbParam,'&retmode=xml&WebEnv=',ncbi.WebEnv,'&query_key=',ncbi.QueryKey]);)

This will read in the file (in XML formatting) as a string, which can be parsed to extract the gene information. REGEXP can be used to parse the string using regular expression.

Best Answer

Related Solutions

MATLAB: Were the ProbeSetNumber and ProbePairNumber columns removed from structs returned by AFFYREAD in MATLAB 7.5 (R2007b)

MATLAB: Am I unable to access the NCBI Entrez Database using GENBANKREAD in MATLAB 7.7 (R2008b)

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