Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets

Takabatake, Kazuki; Izawa, Kazuki; Akikawa, Motohiro; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

doi:10.3390/genes12091455

Open AccessArticle

Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets

by

Kazuki Takabatake

,

Kazuki Izawa

,

Motohiro Akikawa

,

Keisuke Yanagisawa

,

Masahito Ohue

and

Yutaka Akiyama

^*

Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan

^*

Author to whom correspondence should be addressed.

Genes 2021, 12(9), 1455; https://doi.org/10.3390/genes12091455

Submission received: 19 July 2021 / Revised: 17 September 2021 / Accepted: 18 September 2021 / Published: 21 September 2021

(This article belongs to the Special Issue Selected Papers from the 10th International Conference on Bioinformatics and Biomedical Science (ICBBS2021))

Download

Browse Figures

Versions Notes

Abstract

Metagenomic analysis, a technique used to comprehensively analyze microorganisms present in the environment, requires performing high-precision homology searches on large amounts of sequencing data, the size of which has increased dramatically with the development of next-generation sequencing. NCBI BLAST is the most widely used software for performing homology searches, but its speed is insufficient for the throughput of current DNA sequencers. In this paper, we propose a new, high-performance homology search algorithm that employs a two-step seed search strategy using multiple reduced amino acid alphabets to identify highly similar subsequences. Additionally, we evaluated the validity of the proposed method against several existing tools. Our method was faster than any other existing program for ≤120,000 queries, while DIAMOND, an existing tool, was the fastest method for >120,000 queries.

Keywords: homology search; genome sequence; metagenomic analysis; reduced amino acid

Share and Cite

MDPI and ACS Style

Takabatake, K.; Izawa, K.; Akikawa, M.; Yanagisawa, K.; Ohue, M.; Akiyama, Y. Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets. Genes 2021, 12, 1455. https://doi.org/10.3390/genes12091455

AMA Style

Takabatake K, Izawa K, Akikawa M, Yanagisawa K, Ohue M, Akiyama Y. Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets. Genes. 2021; 12(9):1455. https://doi.org/10.3390/genes12091455

Chicago/Turabian Style

Takabatake, Kazuki, Kazuki Izawa, Motohiro Akikawa, Keisuke Yanagisawa, Masahito Ohue, and Yutaka Akiyama. 2021. "Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets" Genes 12, no. 9: 1455. https://doi.org/10.3390/genes12091455

APA Style

Takabatake, K., Izawa, K., Akikawa, M., Yanagisawa, K., Ohue, M., & Akiyama, Y. (2021). Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets. Genes, 12(9), 1455. https://doi.org/10.3390/genes12091455

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Menu

Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets

Abstract

Share and Cite

Article Metrics

Article Access Statistics

Further Information

Guidelines

MDPI Initiatives

Follow MDPI