Clustering genomic words in human DNA using peaks and trends of distributions

Ana Helena Tavares*, Jakob Raymaekers, Peter J. Rousseeuw, Paula Brito, Vera Afreixo

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each distribution into a baseline and a peak distribution. An outlier-robust fitting method is used to estimate the baseline distribution (the 'trend'), and a sparse vector of detrended data captures the peak structure. A simulation study demonstrates the effectiveness of the clustering procedure in grouping distributions with similar peak behavior and/or baseline features. The procedure is applied to investigate similarities between the distribution patterns of genomic words of lengths 3 and 5 in the human genome. These experiments demonstrate the potential of the new method for identifying words with similar distance patterns.
Original languageEnglish
Pages (from-to)57-76
JournalAdvances in Data Analysis and Classification
Volume14
Issue number1
DOIs
Publication statusPublished - 1 Mar 2020
Externally publishedYes

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