Applied Biosystems, Inc.
INHERIT is a sequence analysis and assembly package that utilizes the Fast Data Finder (FDF) in a number of unique ways. The FDF is a linear-systolic array designed to search flat text files very fast. INHERIT employs the FDF in database searching, resulting in search times limited only by disk-transfer rates. INHERIT also has a flexible pattern specification language that allows the expression of very complex biological patterns. These patterns can describe genetic motifs that can be used in database searches. Because of its design, the FDF can search the database for these patterns independent of pattern complexity. The FDF is used in sequence assembly by initially screening pairs of fragments for similarity and then excluding those fragments that are below the threshold of similarity from further consideration in assembly algorithm.