Two-step procedure for detecting change points in genomic sequences

Anjum, Arfa and Jaggi, Seema and Lall, Shwetank and Varghese, Eldho and Rai, Anil and Bhowmik, Arpan and Mishra, Dwijesh Chandra (2024) Two-step procedure for detecting change points in genomic sequences. Current Science, 126 (1). pp. 54-58. ISSN 0011-3891

Text Current Science_2024_Eldho Varghese.pdf Restricted to Registered users only Download (988kB) | Please mail the copy request to cmfrilibrary@gmail.com

Abstract

The field of whole genomic studies and investigations is currently focused on change-point detection. Over time, various segmentation techniques have been proposed to identify these change points. To effectively locate segments within a genome, it is helpful to pinpoint the intervals or boundaries between them, which are known as change points. By treating these change points as outliers, they can be identified. The anomalies or outliers in a dataset are the observations which are significantly different from the rest of the observations. They can be attributed to some measurement errors or properties of the data themselves. Studying the fluctuations over different segments also revealed the heterogeneity between consecutive segments. In this paper, anomaly identification approach or influential point detection has been discussed and studied in cow genome data of chromosome 25. Furthermore, the observed anomalies have been confirmed to determine whether or not they are true change points. The two-step technique resulted in the identification of change sites based on observed abnormalities and is efficient in terms of calculation time and cost. This study aims to detect any anomalies in genomic data and determine the exact points at which the data segment significantly differed from the rest of the segments. We have developed relevant R codes for data processing and applied methodologies.

Item Type:	Article
Uncontrolled Keywords:	Anomalies; change points; genomic sequences; segmentation; two-step procedure
Divisions:	CMFRI-Kochi > Marine Capture > Fishery Resources Assessment, Economics and Extension Division Subject Area > CMFRI > CMFRI-Kochi > Marine Capture > Fishery Resources Assessment, Economics and Extension Division CMFRI-Kochi > Marine Capture > Fishery Resources Assessment, Economics and Extension Division Subject Area > CMFRI-Kochi > Marine Capture > Fishery Resources Assessment, Economics and Extension Division
Depositing User:	Arun Surendran
Date Deposited:	17 Jan 2024 10:55
Last Modified:	17 Jan 2024 11:10
URI:	http://eprints.cmfri.org.in/id/eprint/17958

Actions (login required)

View Item