Faster genome mapping method using 4-ary Perfect Linear Code

2015 Fiscal Year Final Research Report

• Project/Area Number: 24650155
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Osaka University
• Principal Investigator: takenaka yoichi 大阪大学, 情報科学研究科, 准教授 (00324830)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Keywords: ゲノム / 完全線形符号 / 次世代シークエンサー

Outline of Final Research Achievements

The emerging of the next generation DNA sequencers enables us to get an extraordinary amount of DNA short sequences and read their bases. The data size comes bigger and bigger year by year and the increase ratio overwhelms the Moore’s law. This requires new algorithms and mechanism to manipulate the short read faster. This research proposed that 4-ary perfect linear code meets the demand. The DNA sequences are coded to one of the code words of the perfect linear code and we proved that it reduces the search space when we try to find DNA subsequences that is one mismatch from the query DNA sequence. Then we have shown that the perfect linear code is useful to genome mapping and metagenome analyses.

Free Research Field

生物情報学