Abstract: The invention relates to a method that efficiently identifies segments of a collection of polypeptides which are similar to a query polypeptide. Candidate alignments of all or part of the query polypeptide with similar amino acid sequences from the collection of polypeptides are first identified using a scalable parallel processing filter algorithm. The candidate alignments are further examined to yield an ordered list of scored alignments. This method enables massive parallel processing with minimized logic requirements and maximized logic utilization to achieve a dramatic reduction in the time required to produce a high quality sequence alignment report with a fraction of the hardware resources required by current methods.

Abstract: A content addressable memory (“CAM”) engine or controller interfaces between a host signal processor (e.g., a microprocessor) and a plurality of known, commercially-available random access memory (“RAM”) devices. The CAM engine configures the RAM as content addressable memory, thereby causing the normally location-addressed RAM to function as CAM. The CAM engine thus allows for the benefits of both RAM and CAM devices, such as speed, density, cost and intuitiveness, without their inherent drawbacks. Further, the CAM engine implements various flexible memory storage configurations for the keys and associations stored in RAM. Also, the CAM engine implements certain algorithms that provide for the hashing of data, for table load and unload capabilities, for proximity matching, for dealing with overflow conditions, and for implementing hierarchical search capabilities.

Abstract: A method and apparatus for determining the longest prefix match in a content addressable memory. A content addressable memory device comprises an application specific integrated circuit which interfaces between a general microprocessor and a random access memory so as to create an associative memory structure which includes transition nodes, significant nodes and arcs. A table including multiple data structures is created in the random access memory by the device for storing prefixes and associated data in a predetermined manner. The table is manipulated by the device in response to commands such as add data, delete data, and search for data by the microprocessor.

Abstract: A content addressable memory (“CAM”) engine or controller interfaces between a host signal processor (e.g., a microprocessor) and a plurality of known, commercially-available random access memory (“RAM”) devices. The CAM engine configures the RAM as content addressable memory, thereby causing the normally location-addressed RAM to function as CAM. The CAM engine thus allows for the benefits of both RAM and CAM devices, such as speed, density, cost and intuitiveness, without their inherent drawbacks. Further, the CAM engine implements various flexible memory storage configurations for the keys and associations stored in RAM. Also, the CAM engine implements certain algorithms that provide for the hashing of data, for table load and unload capabilities, for proximity matching, for dealing with overflow conditions, and for implementing hierarchical search capabilities.