DNA sequences at a glance.

Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital repres...

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Autores principales:	Armando J Pinho, Sara P Garcia, Diogo Pratas, Paulo J S G Ferreira
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/484b7d3293a849eca46d92ac4619de27
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spelling	oai:doaj.org-article:484b7d3293a849eca46d92ac4619de272021-11-18T08:45:17ZDNA sequences at a glance.1932-620310.1371/journal.pone.0079922https://doaj.org/article/484b7d3293a849eca46d92ac4619de272013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24278218/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the "information profile", which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h(-) and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance.Armando J PinhoSara P GarciaDiogo PratasPaulo J S G FerreiraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e79922 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Armando J Pinho Sara P Garcia Diogo Pratas Paulo J S G Ferreira DNA sequences at a glance.
description	Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the "information profile", which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h(-) and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance.
format	article
author	Armando J Pinho Sara P Garcia Diogo Pratas Paulo J S G Ferreira
author_facet	Armando J Pinho Sara P Garcia Diogo Pratas Paulo J S G Ferreira
author_sort	Armando J Pinho
title	DNA sequences at a glance.
title_short	DNA sequences at a glance.
title_full	DNA sequences at a glance.
title_fullStr	DNA sequences at a glance.
title_full_unstemmed	DNA sequences at a glance.
title_sort	dna sequences at a glance.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/484b7d3293a849eca46d92ac4619de27
work_keys_str_mv	AT armandojpinho dnasequencesataglance AT sarapgarcia dnasequencesataglance AT diogopratas dnasequencesataglance AT paulojsgferreira dnasequencesataglance
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DNA sequences at a glance.

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