Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists

Approximate sequence alignment

Given a collection of strings and a query string, the goal of the approximate string matching is to efficiently find the strings in the collection, which are similar to the query string. In this paper, we focus on edit distance as a measure to quantify the similarity between two strings. Existing q-gram based methods use inverted lists to index the q-grams of the given string collection. These methods begin with generating the q-grams of the query string, disjoint or overlapping, and then merge the inverted lists of these q-grams. Several filtering techniques have been proposed to segment inverted lists in order to obtain relatively shorter lists, thus reducing the merging cost. The filtering technique we propose in this thesis, which is called position restricted alignment, combines well known length filtering and position filtering to provide more aggressive pruning. We then provide an indexing scheme that integrates the inverted lists storage with the proposed filter. It enables us to auto-filter the inverted lists. We evaluate the effectiveness of the proposed approach by experiments

String Matching Problems with Parallel Approaches An Evaluation for the Most Recent Studies

In recent years string matching plays a functional role in many application like information retrieval, gene analysis, pattern recognition, linguistics, bioinformatics etc. For understanding the functional requirements of string matching algorithms, we surveyed the real time parallel string matching patterns to handle the current trends. Primarily, in this paper, we focus on present developments of parallel string matching, and the central ideas of the algorithms and their complexities. We present the performance of the different algorithms and their effectiveness. Finally this analysis helps the researchers to develop the better techniques

QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction

In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with simple proof-of-concept examples to target both the genomics research community and quantum application developers in a self-contained manner. The details of the implementation are discussed for the various layers of the quantum full-stack accelerator design. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/prince-ph0en1x/QuASeR.Comment: 24 page

Preliminary specification and design documentation for software components to achieve catallaxy in computational systems

This Report is about the preliminary specifications and design documentation for software components to achieve Catallaxy in computational systems. -- Die Arbeit beschreibt die Spezifikation und das Design von Softwarekomponenten, um das Konzept der Katallaxie in Grid Systemen umzusetzen. Eine Einführung ordnet das Konzept der Katallaxie in bestehende Grid Taxonomien ein und stellt grundlegende Komponenten vor. Anschließend werden diese Komponenten auf ihre Anwendbarkeit in bestehenden Application Layer Netzwerken untersucht.Grid Computing