{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T23:04:40Z","timestamp":1781651080767,"version":"3.54.5"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: To 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.<\/jats:p>\n               <jats:p>Availability: CBrowse is distributed under the GNU General Public License, available at http:\/\/bioinfolab.muohio.edu\/CBrowse\/<\/jats:p>\n               <jats:p>Contact: \u00a0liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts443","type":"journal-article","created":{"date-parts":[[2012,7,13]],"date-time":"2012-07-13T20:44:25Z","timestamp":1342212265000},"page":"2382-2384","source":"Crossref","is-referenced-by-count":8,"title":["CBrowse: a SAM\/BAM-based contig browser for transcriptome assembly visualization and analysis"],"prefix":"10.1093","volume":"28","author":[{"given":"Pei","family":"Li","sequence":"first","affiliation":[{"name":"1 Department of Automation, Xiamen University, Xiamen, Fujian 361005, China, 2Department of Botany, 3Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 4State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China"},{"name":"1 Department of Automation, Xiamen University, Xiamen, Fujian 361005, China, 2Department of Botany, 3Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 4State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, 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