Abstract:
BACKGROUND:Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community. RESULTS:Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria. CONCLUSIONS:JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Seitzer P,Huynh TA,Facciotti MTdoi
10.1186/1471-2105-14-18subject
Has Abstractpub_date
2013-01-16 00:00:00pages
18issn
1471-2105pii
1471-2105-14-18journal_volume
14pub_type
杂志文章abstract:BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-46
更新日期:2009-02-03 00:00:00
abstract:BACKGROUND:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-117
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abstract:BACKGROUND:Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. RESULTS:We ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-114
更新日期:2004-08-23 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2006-12-12 00:00:00
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pub_type: 杂志文章
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更新日期:2017-05-02 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-281
更新日期:2011-07-12 00:00:00
abstract:BACKGROUND:To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms. RESULTS:We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG o...
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pub_type: 杂志文章
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更新日期:2007-03-12 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03639-7
更新日期:2020-07-14 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-265
更新日期:2012-10-15 00:00:00
abstract:BACKGROUND:This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, us...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S10-S3
更新日期:2009-10-01 00:00:00
abstract:BACKGROUND:Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities tha...
journal_title:BMC bioinformatics
pub_type: 指南,杂志文章
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更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2699-3
更新日期:2019-03-04 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-161
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-21
更新日期:2007-01-23 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-76
更新日期:2004-06-09 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-215
更新日期:2010-04-29 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2018-08-29 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2013-01-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2015-02-20 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2019-11-22 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2005-05-24 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2020-01-10 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2011-05-19 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2010-07-21 00:00:00
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更新日期:2006-11-04 00:00:00