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Title
Japanese:結合エネルギーを考慮したゲノムワイドな高速短鎖核酸配列検索手法の開発 
English: 
Author
Japanese: 山崎眞拓, 伊澤和輝, 平田稜, 柳澤渓甫, 大上雅史, 秋山泰.  
English: Mahiro Yamazaki, Kazuki Izawa, 平田稜, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama.  
Language Japanese 
Journal/Book name
Japanese:研究報告バイオ情報学（BIO） 
English: 
Volume, Number, Page 2022-BIO-69    8    1-8
Published date Mar. 3, 2022 
Publisher
Japanese:情報処理学会 
English: 
Conference name
Japanese: 
English: 
Conference site
Japanese: 
English: 
Official URL https://ipsj.ixsq.nii.ac.jp/ej/?action=pages_view_main&active_action=repository_view_main_item_detail&item_id=216918&item_no=1&page_id=13&block_id=8
 
Abstract The binding energy between nucleic acid sequences is an important factor in considering the binding stability of nucleic acids. Although various methods exist, no method is dedicated for short sequences. The binding energy estimation of short sequences is needed to develop antisense oligonucleotide (ASO) drugs, which has a gap region of approximately 10 bases. In this study, we propose a method for short sequences that enumerate sequences and search through target sequences. We compared to RIsearch, a well-known tool, and the proposed method is 60-90 times faster than the previous tool when the query sequence length is 10-14 nucleotides. In addition, the amount of memory usage was 1.4-116.6MB, indicating that the proposed method can be implemented with a personal computer.

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