Seven Bridges Genomics, Inc.

Smith Micro Software, Inc.

Vladimir Semenyuk

Serge Volkoff

Genomic data is written to disk in a compact format by dividing the data into segments and encoding each segment with the smallest number of bits per character necessary for whatever alphabet of characters appears in that segment. A computer system dynamically chooses the segment boundaries for maximum space savings. A first one of the segments may use a different number of bits per character than a second one of the segments. In one embodiment, dividing the data into segments comprises scanning the data and keeping track of a number of unique characters, noting positions in the sequence where the number increases to a power of two, calculating a compression that would be obtained by dividing the genomic data into one of the plurality of segments at ones of the noted positions, and dividing the genomic data into the plurality of segments at the positions that yield the best compression.

Systems and methods for sequence encoding, storage, and compression

Methods of the invention include representing biological data in a memory subsystem within a computer system with a data structure that is particular to a location in the memory subsystem and serializing the data structure into a stream of bytes that can be deserialized into a clone of the data structure. In a preferred genomic embodiment, the biological data comprises genomic sequences and the data structure comprises a genomic directed acyclic graph (DAG) in which objects have adjacency lists of pointers that indicate the location of any object adjacent to that object. After serialization and deserialization, the clone genomic DAG has the same structure as the original to represent the same sequences and relationships among them as the original.

Biological graph or sequence serialization

The invention provides methods for analyzing sequence data in which a large amount and variety of reference data are efficiently modeled as a reference graph, such as a directed acyclic graph (DAG). The method includes determining positions of k-mers within a reference graph that represents a genomic sequence and known variation, storing the positions of each k-mer in a table entry indexed by a hash of that k-mer, and identifying a region within the reference graph that includes a threshold number of the k-mers by reading from the table entries indexed by hashes of substrings of a subject sequence. The subject sequence may subsequently be mapped to the candidate region.

Systems and methods for genomic pattern analysis

A method of compressing sorted data representation symbols sequentially. Steps include determining whether a symbol currently being encoded is identical to an immediately preceding symbol; encoding the result as a binary event; if the symbols are identical, encoding the symbol ends; if the symbols are different and there is a constant difference between several previous pairs of symbols, determining whether the difference between the current symbol a and the symbol immediately preceding it b is the same as the difference between the symbol b and the symbol immediately preceding it c, and encoding the determination result as another binary event; in the case of positive result of the latest determination, encoding the symbol ends; otherwise, encoding the symbol using a bitwise operation in which bits of the symbol's binary representation are processed sequentially from the most significant bit to the least significant bit. A corresponding decompression method is provided.

Efficient compression method for sorted data representations

A method of separating data blocks with stationary informational characteristics, including the steps of sequentially collecting statistics for small data blocks in an input data set, calculating the relative change in the estimated compression efficiency for a solid block currently being formed caused by merging its statistics with the statistics of a next small block, deciding whether the small block should be added to the solid block; for any block for which the decision is no, the block is used as the starting block of the next solid block to be formed. Auxiliary block data type detection is used to improve the method.

Growing community of inventors

Pacific Grove, CA, United States of America

Vladimir Semenyuk