Genome-wide search of nucleosome patterns using visual analytics

Abstract Motivation The Burrows-Wheeler transform (BWT) is widely used for the fast alignment of high-throughput sequence data. This method also has potential applications in other areas of bioinformatics, and it can be specially useful for the fast searching of patterns on coverage data from different sources. Results We present a nucleosome pattern search method that converts levels of nucleosomal occupancy to a sequence-like format to which BWT searches can be applied. The method is embedded in a nucleosome map browser, ‘Nucleosee‘, an interactive visual tool specifically designed to enhance BWT searches, giving them context and making them suitable for visual discourse analysis of the results. The proposed method is fast, flexible and sufficiently generic for the exploration of data in a broad and interactive way. Availability and implementation The proposed algorithm and visual browser are available for testing at http://cpg3.der.usal.es/nucleosee. The source code and installation packages are also available at https://github.com/rodrigoSantamaria/nucleosee. Supplementary information Supplementary data are available at Bioinformatics online.

[1]  Cizhong Jiang,et al.  Nucleosome positioning and gene regulation: advances through genomics , 2009, Nature Reviews Genetics.

[2]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[3]  Lothar Thiele,et al.  A systematic comparison and evaluation of biclustering methods for gene expression data , 2006, Bioinform..

[4]  Luis Quintales,et al.  Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome , 2016, Genome research.

[5]  Peter J. Park,et al.  HiGlass: Web-based visual comparison and exploration of genome interaction maps , 2017 .

[6]  William Stafford Noble,et al.  Software tools for visualizing Hi-C data , 2016, Genome Biology.

[7]  Oscar Westesson,et al.  Visualizing next-generation sequencing data with JBrowse , 2013, Briefings Bioinform..

[8]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[9]  Liqun Xi,et al.  Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning , 2013, Proceedings of the National Academy of Sciences.

[10]  Ann E. Loraine,et al.  The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets , 2009, Bioinform..

[11]  Yong Zhang,et al.  DNA sequence compression using the Burrows-Wheeler Transform , 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

[12]  Christopher Andrews,et al.  The human is the loop: new directions for visual analytics , 2014, Journal of Intelligent Information Systems.

[13]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[14]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[15]  Zhaoyu Li,et al.  DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing , 2013, Genome research.

[16]  Hanspeter Pfister,et al.  HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples , 2017, bioRxiv.

[17]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[18]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[19]  Vladimir B. Teif,et al.  Nucleosome positioning: resources and tools online , 2015, Briefings Bioinform..

[20]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[21]  D. J. Wheeler,et al.  A Block-sorting Lossless Data Compression Algorithm , 1994 .

[22]  Pavel A. Pevzner,et al.  Bioinformatics Algorithms: An Active Learning Approach , 2014 .

[23]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.