Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: The invention provides systems and methods for encoding specific portions of a genomic graph in a way that is useful for copying or moving those portions from one location to another. The genomic graph can comprise nodes connected by edges, wherein the nodes and edges are stored as edge objects in non-transitory memory of a computer system and wherein an edge within the graph represents a genomic sequence. In on embodiment, the a method of encoding a genomic graph comprises selecting at least one edge from the genomic graph, the at least one edge representing a single genetic sequence and having a position on the genomic graph. The method can further comprise encoding the at least one edge as a string of bits, in which at least a first component of the string of bits stores at least a portion of the position of the edge on the genomic graph.

Abstract: A method of aligning a data sequence to one or more reference sequences represented as a sequence variation graph (SVG) is disclosed. The method can comprise receiving one or more alignment candidate regions and corresponding ordered seeding information. For each of the received alignment candidate regions, a current seed is determined, the current seed being a next-in-order unprocessed seed based on the ordered seeding information. Data paths in the alignment candidate region are then traversed to identify potential next seeds relative to the current seed. If at least one potential next seed is found, a next seed is selected and alignment results are generated by applying a local alignment procedure to align query data in portions of the query data sequence between the current seed and the next seed with reference data in portions of the alignment candidate region located between the current seed and the next seed.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: A method for effective color modeling for predictive image encoding. Colors are processed on a binary basis, when each color index is treated as a binary value. Binary digits are processed sequentially with the use of context-based approach. The context is calculated as a unique combination of binary values of already processed digits, the position of the digit currently being processed and an additional identifier from a limited set of identifiers that describe differences between the predicted color index and the averaged color index being reconstructed during bitwise processing. Color mapping, table operations and a special rules for efficient difference identification are proposed as major enhancements of the method.

Abstract: A video codec for real-time encoding/decoding of digitized video data with high compression efficiency, comprising a frame encoder receiving input frame pixels; a codec setting unit for setting and storing coding setting parameters; a CPU load controller for controlling desired frame encoding time and CPU loading; a rate controller for controlling frame size; a coding statistics memory for storing frequency tables for arithmetic coding of bitstream parameters and a reference frame buffer for storing reference frames. The frame encoder comprises a motion estimation unit, a frame head coding unit, a coded frame reconstruction and storage unit and a macroblock encoding unit. The macroblock encoding unit provides calculation of texture prediction and prediction error, transforming texture prediction error and quantization of transform coefficient, calculation of motion vector prediction and prediction error and arithmetic context modeling for motion vectors, header parameters and transform coefficients.

Abstract: The invention provides a method and apparatus for coding information that is specifically adapted for smaller presentation formats, such as in a hand held video player. The invention addresses, inter alia, reducing the complexity of video decoding, implementation of an MP3 decoder using fixed point arithmetic, fast YcbCr to RGB conversion, encapsulation of a video stream and an MP3 audio stream into an AVI file, storing menu navigation and DVD subpicture information on a memory card, synchronization of audio and video streams, encryption of keys that are used for decryption of multimedia data, and very user interface (UI) adaptations for a hand held video player that implements the improved coding invention herein disclosed.

Abstract: The invention provides a method and apparatus for coding information (FIG. 5) that is specially adapted for smaller presentation formats, such as in a hand held video player (FIG. 1). The invention addresses, inter alia, reducing the complexity of video decoding (55), implementation of an MP3 decoder (56) using fixed point arithmetic, fast YcbCr to RGB conversion, encapsulation of a video stream and an MP3 audio stream into an AVI file, storing menu navigation and DVD subpicture information on a memory card, synchronization of audio and video stream, encryption of keys that are used for decryption of multimedia data (FIG. 3), and very user interface (UI) adaptations for a hand held video player that implements the improved coding invention herein disclosed.

Abstract: The invention provides a method and apparatus for coding information that is specifically adapted for smaller presentation formats, such as in a hand held video player. The invention addresses, inter alia, reducing the complexity of video decoding, implementation of an MP3 decoder using fixed point arithmetic, fast YcbCr to RGB conversion, encapsulation of a video stream and an MP3 audio stream into an AVI file, storing menu navigation and DVD subpicture information on a memory card, synchronization of audio and video streams, encryption of keys that are used for decryption of multimedia data, and very user interface (UI) adaptations for a hand held video player that implements the improved coding invention herein disclosed.

Abstract: The invention provides a method and apparatus for coding information that is specifically adapted for smaller presentation formats, such as in a hand held video player. The invention addresses, inter alia, reducing the complexity of video decoding, implementation of an MP3 decoder using fixed point arithmetic, fast YcbCr to RGB conversion, encapsulation of a video stream and an MP3 audio stream into an AVI file, storing menu navigation and DVD subpicture information on a memory card, synchronization of audio and video streams, encryption of keys that are used for decryption of multimedia data, and very user interface (UI) adaptations for a hand held video player that implements the improved coding invention herein disclosed.

Abstract: The invention provides a method and apparatus for coding information that is specifically adapted for smaller presentation formats, such as in a hand held video player. The invention addresses, inter alia, reducing the complexity of video decoding, implementation of an MP3 decoder using fixed point arithmetic, fast YcbCr to RGB conversion, encapsulation of a video stream and an MP3 audio stream into an AVI file, storing menu navigation and DVD subpicture information on a memory card, synchronization of audio and video streams, encryption of keys that are used for decryption of multimedia data, and very user interface (UI) adaptations for a hand held video player that implements the improved coding invention herein disclosed.

Abstract: The invention provides a method and apparatus for coding information that is specifically adapted for smaller presentation formats, such as in a hand held video player. The invention addresses, inter alia, reducing the complexity of video decoding, implementation of an MP3 decoder using fixed point arithmetic, fast YcbCr to RGB conversion, encapsulation of a video stream and an MP3 audio stream into an AVI file, storing menu navigation and DVD subpicture information on a memory card, synchronization of audio and video streams, encryption of keys that are used for decryption of multimedia data, and very user interface (UI) adaptations for a hand held video player that implements the improved coding invention herein disclosed.