Sri International

Peter D Karp

Patrick Denis Lincoln

Lawrence Robert Toll

Kemal Sonmez

Steven Mark Eker

Pedro Romero

Biological and chemical systems are represented as a symbolic model. Minimal sets of elements of the system are identified from the model, for example, by automatic inference. The model can be constructed from Boolean propositions that are mapped to a binary decision diagram. The model can also be probed using a branch and bound algorithm.

Modeling and evaluation metabolic reaction pathways and culturing cells

Disclosed are methods, software, and systems for comparing biopolymer sequences. The model includes at least two different characterizations of states of matching between segments of sequences at defined positions. Examples of states of matching include: similarity and dissimilarity between objects, as well as similarity to a reference, e.g., a reference sequence or a sequence profile. A topology of particular match states can be used to identify classes of sequences, e.g., preprohormone sequences.

Biopolymer sequence comparison

A model is used to represent a set of structured data objects that include elements at defined positions. The model includes distributions of vectors, each distribution corresponding to particular positions in the respective structured data objects, each of the vectors comprising values for the particular positions; and comparing a given set of structured data objects to the model to determine a likelihood that the given set is represented by the model. At least some of the distributions of the model differ such that different states of matching are indicated. Distributions of the model can indicate: dissimilarity between the structured data objects at defined positions; similarity between the structured data objects at defined positions; or similarity to a reference structure data object at defined positions.

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San Mateo, CA, United States of America

Peter D Karp