Setting Similarity Matrix in MBF

May 24, 2011 at 12:32 AM


I am using Bio library (MBF 2.0) for sequence alignment, and I have a general Question.  While we can select various options for an aligner, such as Gap Open Cost, etc, including similarity matrix, I cannot tell exactly where the matrix data comes from.  For example, if I choose Blosum50 as my similarity matrix, where is this matrix actually constructed that the algorithm will look for by default.  Is each and every algorithm creates a matrix based on the options specified on the fly?

If you can show me exactly where in Bio.dll this is constructed or selected, I would greatly appreciate it.  I know you set similarity matrix that an aligner will use, but where is this matrix?

Thank you, KPOnCodeplex2011

May 24, 2011 at 10:55 PM
Hi kponcodeplex2011
One of our Developers gave me the below infromation: 
We have 11 well defined Similarity Matrices in Bio.dll. These matrices are constructed from the resource files (.txt). You can find the .txt files under ….Bio\Source\Framework\Bio\SimilarityMatrices\Resources\SimilarityMatrices. We have generic class SimilarityMatrix which does the construction based our  StandardSimilarityMatrix enum.
sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
This will get you Blosum50 matrix.
We also support custom matrix by passing your file. Currently, we support ('\t', ' ', ',') delimited matrix files.
SimilarityMatrix sm = new SimilarityMatrix(blosumFilePath);

Please let me know if you need any more clarification.

Fadi Fakhouri on behalf of the MBF Team