Abstract: Roughly described, a database searching method for searching a database, in which hits are ranked in dependence upon an information measure of itoms shared by both the hit and the query. The information measure can be a Shannon information score, or another measure which indicates the information value of the shared itoms. An itom can be a word or other token, or a multi-word phrase, and can overlap with each other. Synonyms can be substituted for itoms in the query, with the information measure of substituted itoms being derated in accordance with a predetermined measure of the synonyms' similarity. Indirect searching methods are described in which hit from other search engines are re-ranked in dependence upon the information measures of shared itoms. Structured and completely unstructured databases may be searched, with hits being demarcated dynamically. Hits may be clustered based upon distances in an information-measure-weighted distance space.

Abstract: Systems and methods for generating indexes and fast searching of “approximate”, “fuzzy”, or “homologous” matches for a large quantity of data in a metric space are provided. The data is indexed to generate a search tree taxonomy. Once the index is generated, a query can be provided to report all hits within a certain neighborhood of the query. In an even faster implementation, the invention may be used together with existing approximate sequence comparison algorithms, such as FASTA and BLAST. Here, a local distance of a local metric space is used to generate local search tree branches. Applications of this invention may include homology search for DNA and/or protein sequences, textual or byte-based searches, literature search based on lists of keywords, and vector and matrix based indexing and searching.