Reduced memory nucleotide sequence comparison

Abstract

Comparisons between two nucleotide sequences can be performed by customized integrated circuity that can implement a Smith Waterman analysis in a reduced memory footprint, storing and referencing onlyindividual portions, or subsections, of a two-dimensional matrix that is representative of the comparison between the two nucleotide sequences. As the backtracking proceeds, backtracking metadata corresponding to a cell from a subsection that is not currently retained in memory can be required. Such a subsection can be regenerated from previously generated scores associated with checkpoint cellsof the two-dimensional matrix that comprise two edges of the subsection being regenerated. Moreover, to further reduce memory consumption, the backtracking metadata stored for each cell can comprise four binary digits: two indicative of a directional assignment, one indicative of whether the corresponding cell is part of a deletion stretching across multiple contiguous cells, and one analogously indicative of insertions stretching across multiple contiguous cells.

Description

Background technique [0001] A special-purpose processing device may include processing circuitry that is preconfigured to perform a discrete set of computational operations faster than a general-purpose central processing unit. An application-specific integrated circuit (ASIC) includes a system of integrated circuits that is specifically designed to perform a specific set of operations or calculations such that such operations or calculations can be performed faster or more efficiently than a general-purpose central processing unit. Field Programmable Gate Arrays (FPGAs) also include integrated circuit systems, usually in the form of programmable logic blocks composed of individual microprocessor gates and other similar integrated circuits that can be programmed or A collection of operations or calculations designed to perform specific operations or calculations faster or more efficiently than a general-purpose central processing unit. [0002] One area in which computations ...

AI Technical Summary

Problems solved by technology

However, as those skilled in the art will appreciate, accessing such memory is substantially slower than accessing a memory located on the same chip (such as the same ASIC or FPGA whose circuitry is performing the comparison between pairs of nucleotide sequences). memory is slower

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