Thomas G. Marr

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Suppose you are given a set of natural entities (e.g., proteins, organisms, weather patterns, etc.) that possess some important common externally observable properties. You also have a structural description of the entities (e.g., sequence, topological, or geometrical data) and a distance metric. Combinatorial pattern discovery is the activity of finding(More)
We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) find candidate motifs in a small sample of the sequences; (2) test whether these motifs are approximately present in all the sequences. To reduce the running time, we develop two optimization heuristics based on(More)
We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) nd candidate motifs in a small sample of the sequences; (2) test whether these motifs are approximately present in all the sequences. To reduce the running time, we develop two optimization heuristics based on(More)
We propose a generating functional method--random path analysis (RPA)--that generalizes the classical dynamic programming (DP) method widely used in sequence alignments. For a given cost function, DP is a deterministic method that finds an optimal alignment by minimizing the total cost function for all possible alignments. By allowing uncertainty, RPA is a(More)
We have studied five methods of protein classification and have applied them to the 768 groups of related proteins in the PROSITE catalog. Four of these methods are based on searching a database of blocks, and the other uses the frequently occurring motifs found in the protein families combined with a fingerprint technique. Our experimental results show(More)
DNA is a long biopolymer that is found in the nucleus of every living cell. The DNA of a cell contains the genetic information that determines every physical aspect of an individual. This information is encoded in the sequence pattern of four different heterocyclic molecules called nucleotides, which are the building blocks of the DNA polymer. Such traits(More)
One of the goals of the Human Genome Project is to produce libraries of largely contiguous, ordered sets of molecular clones for use in sequencing and gene mapping projects. This is planned to be done for human and many model organisms. Theory and practice have shown that long-range contiguity and the degree to which the entire genome is covered by ordered(More)
We announce the formation of an International Mammalian Genome Society to promote and coordinate the experimental genetic study of mammals, including comparative mapping, gene regulation, and molecular genetics. The major purpose of the society will be to provide a more formal mechanism of communication for investigators interested in mammalian genetics and(More)