An overview of MochiView's regulatory motif analysis and management tools. (a) MochiView provides a simple interface for browsing and annotating a motif library. (b) MochiView provides numerous utilities for importing and exporting motif frequency matrices and logos, including support for motifs based on degenerate DNA sequences, frequency matrices, or affinity matrices (as produced by the program MatrixREDUCE ). (c) MochiView contains a motif detection utility that can identify de novo motifs enriched in user-defined regions. (d) A motif comparison tool identifies similarities between newly discovered motifs and those in the motif library. (e) Two utilities are provided for analyzing motif enrichment in sets of user-defined regions. (f) Utilities are provided for detecting non-random distribution of motifs relative to either a set of user-defined locations (for example, start codons or peaks of ChIP enrichment) or strong instances of another motif (for example, co-occurring motifs that are typically separated by a 25 bp gap). (g) Several utilities are provided for scoring motifs against user-defined regions. For example, it is relatively simple to output a file containing the top motif score upstream of each gene for every motif in the library. (h) Enrichment for Gene Ontology terms can be determined for genes with upstream sequence that contains a strong instance of a motif.