Shape-based alignment of genomic landscapes in multi-scale resolution.

Nucleic Acids Research
Hiroki AshidaMichiaki Hamada

Abstract

Due to dramatic advances in DNA technology, quantitative measures of annotation data can now be obtained in continuous coordinates across the entire genome, allowing various heterogeneous 'genomic landscapes' to emerge. Although much effort has been devoted to comparing DNA sequences, not much attention has been given to comparing these large quantities of data comprehensively. In this article, we introduce a method for rapidly detecting local regions that show high correlations between genomic landscapes. We overcame the size problem for genome-wide data by converting the data into series of symbols and then carrying out sequence alignment. We also decomposed the oscillation of the landscape data into different frequency bands before analysis, since the real genomic landscape is a mixture of embedded and confounded biological processes working at different scales in the cell nucleus. To verify the usefulness and generality of our method, we applied our approach to well investigated landscapes from the human genome, including several histone modifications. Furthermore, by applying our method to over 20 genomic landscapes in human and 12 in mouse, we found that DNA replication timing and the density of Alu insertions are highly ...Continue Reading

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Citations

Nov 28, 2012·American Journal of Human Genetics·Amnon KorenSteven A McCarroll
Feb 19, 2019·Nucleic Acids Research·Tanmoy Roychowdhury, Alexej Abyzov
Sep 26, 2017·Genome Biology and Evolution·Reuben M BuckleyDavid L Adelson
Mar 3, 2017·BMC Evolutionary Biology·Vladimir N BabenkoYuriy L Orlov

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Datasets Mentioned

BETA
GSE30340

Methods Mentioned

BETA
Hi-C

Software Mentioned

GeLATo Alignment
BLAST
LAST
RepeatMasker
BLAT
UCSC genome browser
BLASTZ
Linux
GeLATo
ENCODE

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