NDLI: Application of signal processing for DNA sequence compression

Content Provider	IET Digital Library
Author	Law, Bonnie Ngai Fong
Abstract	Due to the advancement of high-throughput sequencing technologies, it is now feasible for sequencing individual genomes in a fast and affordable manner. With the significant increase in the number of individual genomes, compression methods are needed to reduce pressure on data storage as well as enable effective data distribution and management. The compression methods can generally be divided into two classes, namely reference-free methods and reference-based methods. In reference-free methods, redundancies within the target DNA sequence to be compressed are explored. In reference-based methods, redundancies between the target DNA sequence and other reference sequences are identified to achieve compression. This type of method is applicable to population sequences which are highly similar to each other and have a small number of mismatches. Some of the methods can also be applied to partially similar sequences such as chromosome sequences or sequences having evolutionary relationship. The authors highlight recent developments in these methods. In the comparative study, the authors’ simulation results reveal that the selection of a reference sequence is a crucial factor affecting the compression performance. Use of multiple number of reference sequences and enhancement strategies such as reference rewriting are important to achieve a large compression gain.
Starting Page	569
Ending Page	580
Page Count	12
ISSN	17519675
Volume Number	13
e-ISSN	17519683
Issue Number	Issue 6, Aug (2019)
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/iet-spr/13/6
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/10.1049/iet-spr.2018.5392
Journal	IET Signal Processing
Publisher	The Institution of Engineering and Technology
Publisher Date	2019-05-23
Access Restriction	Open
Rights License	Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/)
Subject Keyword	Bioinformatics Biology And Medical Computing Compression Method Data Compression Data Distribution Data Handling Technique Data Management Digital Signal Processing DNA DNA Sequence Compression Genetics Genomics High-throughput Sequencing Technology Individual Genomes Reference Sequence Reference-based Method Reference-free Method Signal Processing Signal Processing And Detection
Content Type	Text
Resource Type	Article
Subject	Signal Processing Electrical and Electronic Engineering

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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