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dc.contributor.authorLi, Pei
dc.contributor.authorJi, Guoli
dc.contributor.author吉国力
dc.contributor.authorDong, Min
dc.contributor.authorSchmidt, Emily
dc.contributor.authorLenox, Douglas
dc.contributor.authorChen, Liangliang
dc.contributor.authorLiu, Qi
dc.contributor.authorLiu, Lin
dc.contributor.authorZhang, Jie
dc.contributor.authorLiang, Chun
dc.date.accessioned2013-01-21T00:57:11Z
dc.date.available2013-01-21T00:57:11Z
dc.date.issued2012-09-15
dc.identifier.citationBIOINFORMATICS.2012,28(18):2382-2384zh_CN
dc.identifier.issn1367-4803
dc.identifier.urihttp://dx.doi.org/10.1093/bioinformatics/bts443
dc.identifier.uriWOS:000308532300061
dc.identifier.urihttps://dspace.xmu.edu.cn/handle/2288/14602
dc.description.abstractTo address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects.zh_CN
dc.description.sponsorshipNIH-AREA [1R15GM94732-1 A1]; Key Project of Chinese National Programs for Fundamental Research and Development (973 Program) [2009CB118902]; National Natural Science Foundation of China [61174161]; Specialized Research Fund for the Doctoral Program of Higher Education of China [20090121110022]; Fundamental Research Funds for the Central Universities in China (Xiamen University) [2011121047, 201112G018, CXB2011035]zh_CN
dc.language.isoenzh_CN
dc.publisherOXFORD UNIV PRESSzh_CN
dc.subjectGENOME BROWSERzh_CN
dc.subjectANNOTATIONzh_CN
dc.subjectMAPzh_CN
dc.titleCBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysiszh_CN
dc.typeArticlezh_CN


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