Abstract: Each of a plurality of substantially co-linear alignments has a score. Each alignment may comprise a starting alignment that has been diagonally extended to meet a length requirement. Dynamic programming is performed in interalignment regions between the extended alignments to generate a corresponding set of interalignment scores. Alignment scores and interalignment scores are summed to generate a score for the entire chain of alignments. This process is repeated for multiple chains. Chains of alignments are ranked by chain score and are displayed to a user. In one embodiment, additional dynamic programming is performed at the head and tail of each chain to increase the chain score when possible. An integrated circuit that performs the method at high speed in hardware is disclosed. Techniques are disclosed that reduce the amount of interalignment dynamic programming. The method increases sensitivity and gives an order of magnitude speed improvement over NCBI-BLAST.

Abstract: Each of a plurality of substantially co-linear alignments has a score. Each alignment may comprise a starting alignment that has been diagonally extended to meet a length requirement. Dynamic programming is performed in interalignment regions between the extended alignments to generate a corresponding set of interalignment scores. Alignment scores and interalignment scores are summed to generate a score for the entire chain of alignments. This process is repeated for multiple chains. Chains of alignments are ranked by chain score and are displayed to a user. In one embodiment, additional dynamic programming is performed at the head and tail of each chain to increase the chain score when possible. An integrated circuit that performs the method at high speed in hardware is disclosed. Techniques are disclosed that reduce the amount of interalignment dynamic programming. The method increases sensitivity and gives an order of magnitude speed improvement over NCBI-BLAST.

Abstract: A biomolecular sequence database is encoded using a set of byte-aligned block codes. Some of the block codes encode a portion of a current sequence by pointing to an identical portion of another sequence. Others of the block codes are run length codes. Multiple different ways of encoding a current sequence using different ones of the block codes are determined. Dynamic programming is used to determine which one of these ways most efficiently encodes the current sequence into the shortest string of block codes. Each sequence in the database is encoded as such a string of block codes.

Abstract: An apparatus produces an encoded and compressed digital data stream from an original input digital data stream using a forward discrete wavelet transform and a tree encoding method. The input digital data stream may be a stream of video image data values in digital form. The apparatus is also capable of producing a decoded and decompressed digital data stream closely resembling the originally input digital data stream from an encoded and compressed digital data stream using a corresponding tree decoding method and a corresponding inverse discrete wavelet transform. A dual convolver is disclosed which performs both boundary and nonboundary filtering for forward transform discrete wavelet processing and which also performs filtering of corresponding inverse transform discrete wavelet processes. A portion of the dual convolver is also usable to filter an incoming stream of digital video image data values before forward discrete wavelet processing.

Abstract: A decompression method uses four coefficient inverse perfect reconstruction digital filters. The coefficients of these inverse perfect reconstruction digital filters require a small number of additions to implement thereby enabling rapid decompression in software. The method partially inverse transforms a sub-band decomposition to generate a small low pass component image. This small image is expanded in one dimension by performing interpolation on the rows of the small image and is expanded in a second dimension by replicating rows of the interpolated small image. Transformed chrominance data values may be inverse transformed using inverse perfect reconstruction digital filters having a fewer number of coefficients than the inverse perfect reconstruction digital filters used to inverse transform the corresponding transformed luminance data values.

Abstract: A compression and decompression method using a wavelet decomposition, frequency based tree encoding, tree based motion encoding, frequency weighted quantization, Huffman encoding, and tree based activity estimation for bit rate control. Forward and inverse quasi-perfect reconstruction transforms are used to generate the wavelet decomposition and to reconstruct data values close to the original data values. The forward and inverse quasi-perfect reconstruction transforms utilize special filters at the boundaries of the data being transformed and/or inverse transformed.