Abstract: A method and system for conducting sequence searches in a sequence database wherein in one embodiment, the method includes: combining a plurality of query sequences into a combined query sequence; determining a plurality of subdivisions of the sequence database; performing a plurality of searches, wherein each search includes a comparison of the combined query sequence against one of the plurality of subdivisions of the database to produce a plurality of word matches; extending the length of the plurality of word matches to produce a plurality of High-scoring Segment Pairs, combining the plurality of High-scoring Segment Pairs; and producing a plurality of reports, each report representing the highest scoring matches for one of the plurality of query sequences.

Abstract: A system and method for improving the accuracy of DNA sequencing and error probability estimation through application of a mathematical model to the analysis of electropherograms. The method includes processing a plurality of information obtained from a base calling system and creating a plurality of refined base calls using a plurality of original base calls and a plurality of intrinsic peak characteristics. A quality value is also assigned to each of the plurality of refined base calls using the plurality of intrinsic peak characteristics. Processing comprises detecting a plurality of peaks, expanding the plurality of peaks, and resolving the plurality of expanded peaks. Resolving may include fitting the plurality of expanded peaks using a model of a peak shape. A peak resolution parameter is calculated and used in processing. The system may also be trained.

Abstract: A system and method for improving the accuracy of DNA sequencing and error probability estimation through application of a mathematical model to the analysis of electropherograms. The method includes processing a plurality of information obtained from a base calling system and creating a plurality of refined base calls using a plurality of original base calls and a plurality of intrinsic peak characteristics. A quality value is also assigned to each of the plurality of refined base calls using the plurality of intrinsic peak characteristics. Processing comprises detecting a plurality of peaks, expanding the plurality of peaks, and resolving the plurality of expanded peaks. Resolving may include fitting the plurality of expanded peaks using a model of a peak shape. A peak resolution parameter is calculated and used in processing. The system may also be trained.

Abstract: A programmable, special-purpose, pipeline processing system for processing dynamic programming algorithms. The pipeline processing system includes a plurality of accelerator chips coupled in series. The first and last accelerator chips are coupled to interface logic. Each of the accelerator chips includes an instruction processor; a plurality of pipeline processor segments coupled in series. Each of the pipeline processor segments includes a plurality of pipeline processors coupled in series. Each of the pipeline processors has an output and has as one input an output from a preceding pipeline processor and, as a set of second inputs, a corresponding set of outputs from the instruction processor. Also provided is a result processor having an output, and having as one input, an output from a prior result processor, and, as a second input, the output from one of the plurality of pipeline processors.