MATLAB: Is the structure created from a GenBank-file within the Bioinformatics Toolbox 1.0 (R13SP1+) missing the “Sequence” information

Bioinformatics Toolboxfilegenbankgenbankreadgetgenbankimportsequence

I am trying to read in data from a GenBank-file using the GETGENBANK function. If I use the example from the function's help:
S = getgenbank('M10051');
the output structure "S" does not include the "Sequence" information. The same problem occurs if I try to read in a GenBank-file that I saved locally, with the GENBANKREAD function.

Best Answer

  • The BASECOUNT line has been removed from GenBank-files in Release 137 format. The GENBANKREAD function, used to read in the GenBank-files, looks for the BASECOUNT line before it reads in the sequence information. If this line is not found, the function stops reading from the file.
    An updated version of the GENBANKREAD function is available here:
    Use it to replace the $MATLAB/toolbox/bioinfo/bioinfo/genbankread.m file (where $MATLAB is the root directory of your MATLAB installation).