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GeNemo: a search engine for web-based functional genomic data

A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data scie...

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Detalles Bibliográficos
Autores principales: Zhang, Yongqing, Cao, Xiaoyi, Zhong, Sheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987887/
https://www.ncbi.nlm.nih.gov/pubmed/27098038
http://dx.doi.org/10.1093/nar/gkw299
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author Zhang, Yongqing
Cao, Xiaoyi
Zhong, Sheng
author_facet Zhang, Yongqing
Cao, Xiaoyi
Zhong, Sheng
author_sort Zhang, Yongqing
collection PubMed
description A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org.
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spelling pubmed-49878872016-08-22 GeNemo: a search engine for web-based functional genomic data Zhang, Yongqing Cao, Xiaoyi Zhong, Sheng Nucleic Acids Res Web Server issue A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org. Oxford University Press 2016-07-08 2016-04-20 /pmc/articles/PMC4987887/ /pubmed/27098038 http://dx.doi.org/10.1093/nar/gkw299 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server issue
Zhang, Yongqing
Cao, Xiaoyi
Zhong, Sheng
GeNemo: a search engine for web-based functional genomic data
title GeNemo: a search engine for web-based functional genomic data
title_full GeNemo: a search engine for web-based functional genomic data
title_fullStr GeNemo: a search engine for web-based functional genomic data
title_full_unstemmed GeNemo: a search engine for web-based functional genomic data
title_short GeNemo: a search engine for web-based functional genomic data
title_sort genemo: a search engine for web-based functional genomic data
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987887/
https://www.ncbi.nlm.nih.gov/pubmed/27098038
http://dx.doi.org/10.1093/nar/gkw299
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