Design of Pipelined Architecture for Biological Sequence Alignment

Abstract

Sequence alignment is crucial for genome analysis because it allows to identify similarities newline in biological sequences. Sequence alignment techniques are used to compare newly gen newlineerated sequences to reference sequences, finding mutations, genetic variants, and other newline significant features. Effective biological sequence alignment depends on the computation newline methods used in pairwise and multiple sequence alignment. Generally, sequence align newlinement is accomplished by employing a computationally intensive dynamic programming newline paradigm. Due to the exponential growth of genome sequences, sequence alignment needs newline acceleration to process in an accurate, high-speed, and efficient manner. newline The purpose of this thesis is to pinpoint the area where present tools, algorithms, newline and hardware are deficient to produce optimal sequence alignment. The thesis first newline identifies pair-wise sequence alignment as the primary method of alignment, dominat newlineing bioinformatics analysis for the massive production of genome data; the huge volume newline of data demands not only prevents efficiency but also raises high run-time memory and newline power consumption. This thesis develops solutions across hardware accelerators to opti newlinemise inference efficiency by jointly considering optimal characteristics, distinctive dynamic newline programming-based model architectures, different pipeline applications, and the underly newlineing hardware in order to address the challenges of designing a unique system for parallelism newline in processing multiple sequences. We have suggested four key works to accomplish these newline objectives. newline A memory-efficient architecture for computationally expensive pair-wise global align newlinement techniques has been proposed to achieve high-throughput processing in hardware newline accelerators. In this approach, the direction matrix with O(jn) space complexity only newline stores 2-bit width information representing directions (diagonal, vertical, horizontal) or newline no movement for the trace-back operation, where j-nucleotide in a query and n-nucleotide newline in a reference sequence. To