Journal
GENES
Volume 13, Issue 11, Pages -Publisher
MDPI
DOI: 10.3390/genes13112005
Keywords
pairwise alignment; bioinformatics; database systems
Categories
Funding
- Application Domain Specific Highly Reliable IT Solutions project
- National Research, Development and Innovation Fund of Hungary, under the Thematic Excellence Programme [TKP2020-NKA-06]
Ask authors/readers for more resources
The article presents a novel approach for comparative analysis of sequences within a database environment, taking advantage of database management systems to expedite alignment algorithms. The authors work with the column-oriented MonetDB and discuss the key benefits of this database system in relation to their proposed heuristic approach.
Biological data have gained wider recognition during the last few years, although managing and processing these data in an efficient way remains a challenge in many areas. Increasingly, more DNA sequence databases can be accessed; however, most algorithms on these sequences are performed outside of the database with different bioinformatics software. In this article, we propose a novel approach for the comparative analysis of sequences, thereby defining heuristic pairwise alignment inside the database environment. This method takes advantage of the benefits provided by the database management system and presents a way to exploit similarities in data sets to quicken the alignment algorithm. We work with the column-oriented MonetDB, and we further discuss the key benefits of this database system in relation to our proposed heuristic approach.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available