Method for analyzing polysaccharides

A method for determining whether monosaccharides or disaccharides of a query sequence match monosaccharides or disaccharides of a polysaccharide, wherein the query sequence is represented by a first data structure, tangibly embodied in a computer-readable medium, including an identifier that includes fields, each field for storing a value for the monosaccharides or disaccharides of the query sequence, and wherein the polysaccharide is represented by a second data structure, tangibly embodied in a computer-readable medium, including an identifier that includes fields, each field for storing a value for the monosaccharides or disaccharides of the polysaccharide, wherein one or more of the values of the second data structure correspond to the nature and degree of sulfation or acetylation of the monosaccharides or disaccharides of the polysaccharide that alone do not provide the identity of the monosaccharides or disaccharides, the method comprising acts of:

• (A) a user providing input for the fields of the first data structure with an input device, wherein one or more of the values of the first data structure correspond to the nature and degree of sulfation or acetylation of the monosaccharides or disaccharides of the query sequence that alone do not provide the identity of the monosaccharides or disaccharides;
• (B) generating masks with the values stored in the fields of the first data structure;
• (C) performing binary operations on the values stored in the fields of the second data structure with the masks to generate results;
• and
• (D) determining whether the monosaccharides or disaccharides of the query sequence match the monosaccharides or disaccharides of the polysaccharide with the results;
• wherein the polysaccharide comprises disaccharide repeat units comprising hexosamine and glucuronic or iduronic acid that are linked by α/β1→4 glycosidic linkages.