Why do I receive an error or an incorrect plot when using DIMERCOUNT in Bioinformatics Toolbox 1.1 (R14)?

I am using the DIMERCOUNT function to count dimers in a sequence that includes gaps and/or ambiguous bases. I receive an error when working with a sequence including gaps (represented with a hyphen), and an incorrect plot while working with sequences including ambiguous bases. For example, when I type the following sequence:

dimercount('TAG-TGGCCAAGCGAGCTTG')

I expect a warning about gaps and/or ambiguous bases, as described in the documentation, and then a list of dimers, including an "Others" field. For the sequence given above, I would expect the following output:

 Warning: Ambiguous symbols '-' appear in the sequence. These will be in Others.

 In dimercount at 132

 ans = 

         AA: 1

         AC: 0

         AG: 3

         AT: 0

         CA: 1

         CC: 1

         CG: 1

         CT: 1

         GA: 1

         GC: 3

         GG: 1

         GT: 0

         TA: 1

         TC: 0

         TG: 2

         TT: 1

     Others: 2

Instead, the DIMERCOUNT function produces an error of the following form:

 ??? Attempted to access buckets(16,16); index out of bounds because size(buckets)=[15,15].

 Error in ==> dimercount at 100

     buckets(dna(count),dna(count+1)) = buckets(dna(count),dna(count+1)) + 1;

 Error in ==> basecount_dimercount_error at 35

 dch=dimercount(mySequence)

If I use a different symbol to represent the gaps, or work with a sequence including ambiguous bases, I do not receive this error. If I use the 'Chart' option with a sequence containing ambiguous bases, however, the "Others" field is missing from the resulting plot.

Answer 1

[MathWorks Support Team]

This bug has been fixed in Release 14 Service Pack 3 (R14SP3). For previous product releases, read below for any possible workarounds:

This problem has been fixed in Bioinformatics Toolbox 2.1 (R14SP2+). For previous versions, read the following:

There is a bug in Bioinformatics Toolbox 1.1 (R14) when using DIMERCOUNT with sequences containing gaps and/or ambiguous bases.

To work around the error produced when working with sequences with gaps, substitute a different character for the hyphen, such as the letter X (which normally does not represent a base) or a space.

There are no known workarounds for the issue with plots.