MotifFinder automatically analyzes glycan array data and create a versatile set of glycan motifs which decipher structural codes representing protein-glycan interactions. It has many features that are not found in any other glycan-array analysis program. It uses a novel framework for representing lectin specificity as a family of motifs organized as primary motifs and fine specificities; each motif is defined using a new syntax that permits precise specifications of the complexity and tolerance of a pattern; the algorithm employs regression trees with simultaneous motif optimization to find the family of motifs that accurately describe binding specificity; it can jointly analyze multiple datasets to increase the completeness and accuracy of the output; and the output formats are usable as standalone results or as inputs to subsequent analyses. In current version of the software, it includes new functions such as mouse-over glycan structure view, Kd output, enabling searching of non-glycan elements (e.g., glycopeptides), and downstream bioinformatics mining.